Package 'genevintage'

Description

Maps each row's transcript identifier with transcript2gene() and sums the rows of each gene. Rows come back in the order their gene was first seen. Columns, column names and the matrix class (dense, sparse Matrix, data frame) are kept.

Usage

aggregate_transcripts(
  x,
  species = NULL,
  release = NULL,
  assembly = NULL,
  source = NULL,
  mapping = NULL,
  row_ids = NULL,
  label = c("id", "name"),
  unmapped = c("keep", "drop"),
  quiet = FALSE
)

AggregateTranscripts(
  x,
  species = NULL,
  release = NULL,
  assembly = NULL,
  source = NULL,
  mapping = NULL,
  row_ids = NULL,
  label = c("id", "name"),
  unmapped = c("keep", "drop"),
  quiet = FALSE
)

Arguments

Details

Summing is right for counts and for TPM; it is not for effective lengths.

Value

x with one row per gene. A warning of class genevintage_unmapped_transcripts is raised when fewer than half the rows mapped; call transcript2gene() and pass its result as mapping to see which ones.

See Also

transcript2gene(), geneid2name().

Examples

tx <- data.frame(
  transcript_id = c("ENSMUST00000000001", "ENSMUST00000000002"),
  id = "ENSMUSG00000000001", name = "Gnai3"
)
m <- matrix(1:6, nrow = 3, dimnames = list(
  c("ENSMUST00000000001.4", "ENSMUST00000000002.1", "ENSMUST00000999999.1"),
  c("s1", "s2")
))
aggregate_transcripts(m, mapping = tx)

Description

Symbol, biotype and coordinates in one table, for genes given as identifiers or as names. The caller's own token comes back in input, so the result joins straight onto a results table or a feature frame.

Usage

annotate_genes(
  ids,
  species = NULL,
  release = NULL,
  assembly = NULL,
  source = NULL,
  mapping = NULL,
  quiet = FALSE
)

AnnotateGenes(
  ids,
  species = NULL,
  release = NULL,
  assembly = NULL,
  source = NULL,
  mapping = NULL,
  quiet = FALSE
)

Arguments

Details

Unmatched inputs are retained with NA columns. Names matching several genes yield a row for each.

Value

A data frame of input, id, name, chr, biotype and, where the annotation carries them, start, end, strand and span. span is the genomic extent from first to last base. See stream_gtf().

See Also

gene_names() for one value per input.

Examples

hs <- read.delim(system.file("extdata", "example_mapping.tsv", package = "genevintage"))
annotate_genes(c("TP53", "ENSG00000198804", "MALAT1"), mapping = hs)

Description

Build a compact species/release gene-symbol index from GTF mappings

Usage

build_symbol_index(mappings, min_release = NULL)

BuildSymbolIndex(mappings, min_release = NULL)

Arguments

Value

A data frame with species, release, assembly, source, and symbol.

Examples

hs <- read.delim(system.file("extdata", "example_mapping.tsv", package = "genevintage"))
hs$species <- "homo_sapiens"
hs$release <- "116"
head(build_symbol_index(hs))

Description

Fetch GTF mappings and build a symbol index

Usage

build_symbol_index_from_gtf(species, releases, source = "ensembl")

BuildSymbolIndexFromGTF(species, releases, source = "ensembl")

Arguments

Value

A symbol index suitable for detect_species_names().

Examples

ix <- build_symbol_index_from_gtf("yeast", releases = 116)

Description

Selects the protein_coding biotype. Immunoglobulin and T-cell receptor segments encode protein too but carry their own biotypes; ask for "immune" through genes_by_biotype() to add them.

Usage

coding_genes(
  ids = NULL,
  species = NULL,
  release = NULL,
  assembly = NULL,
  source = NULL,
  mapping = NULL,
  quiet = FALSE
)

CodingGenes(
  ids = NULL,
  species = NULL,
  release = NULL,
  assembly = NULL,
  source = NULL,
  mapping = NULL,
  quiet = FALSE
)

Arguments

Value

A data frame of id, name, chr and biotype.

See Also

noncoding_genes(), genes_by_biotype().

Examples

hs <- read.delim(system.file("extdata", "example_mapping.tsv", package = "genevintage"))
coding_genes(c("TP53", "MALAT1", "XIST"), mapping = hs)

nrow(coding_genes(species = "human"))

Description

Joins two vintages on the stable identifier and reports what differs: genes the newer release added, genes it dropped, and genes whose symbol or biotype changed. Rows that are identical in both are not returned.

Usage

compare_releases(
  species,
  from,
  to,
  assembly = NULL,
  source = NULL,
  quiet = FALSE
)

CompareReleases(
  species,
  from,
  to,
  assembly = NULL,
  source = NULL,
  quiet = FALSE
)

Arguments

Details

Added and removed genes are identified by stable identifier presence. Finding a successor to a retired identifier requires a separate lookup.

Value

A data frame of id, change ("added", "removed", "renamed" or "retyped"), name_from, name_to, biotype_from and biotype_to.

See Also

detect_release() to find out which vintages you have.

Examples

d <- compare_releases("human", from = 110, to = 116)
table(d$change)
d[d$change == "renamed", ]

Description

Excel silently reinterprets some gene symbols: SEPT9 becomes 9-Sep, MARCH1 becomes 1-Mar, 2310009E13 becomes 2.31E+13. Several symbols can produce the same token, so candidates are checked against the caller's species and release. For example, 9-Sep resolves to SEPT9 against Ensembl release 95 and SEPTIN9 against release 116.

Usage

correct_genenames(
  x,
  species = NULL,
  release = NULL,
  assembly = NULL,
  source = NULL,
  mapping = NULL,
  unique,
  quiet = FALSE,
  row_ids = NULL
)

CorrectGeneNames(
  x,
  species = NULL,
  release = NULL,
  assembly = NULL,
  source = NULL,
  mapping = NULL,
  unique,
  quiet = FALSE,
  row_ids = NULL
)

Arguments

Details

Tokens that are not damaged are returned unchanged, so the result drops straight back into rownames(). A token with no surviving candidate, or with more than one, is also returned unchanged and reported. MARCH1 and MARC1 both become 1-Mar; a candidate already present undamaged elsewhere in x is ruled out, which usually resolves it.

Candidates are checked against an annotation: mapping if given, otherwise species at release. Without release the newest one is used, which returns current HGNC spellings (SEPTIN9, not SEPT9); stable IDs in x are dated instead. Without species, it is detected from stable IDs in x, and bare symbols are refused.

Renames beyond the old spelling come from the species' nomenclature authority: HGNC for human, MGI for mouse, ZFIN for zebrafish (SEP15 to SELENOF, sept9 to septin9a). A mapping without species is read as human nomenclature.

For a matrix, sparse Matrix or data frame, only row names are replaced; dimensions, row order and other attributes are preserved. Call correct_genenames() on rownames(x) to obtain the corrected, ambiguous and unresolved attributes.

Value

If x is a plain vector: a character vector the same length and order as x, carrying a corrected attribute (logical), an ambiguous attribute naming tokens that matched more than one symbol, and an unresolved attribute naming damaged tokens no symbol in this annotation produces. If x is a matrix, sparse Matrix or data frame: the same object with corrected row names and none of those attributes.

References

Ziemann M, Eren Y, El-Osta A (2016). Gene name errors are widespread in the scientific literature. Genome Biology 17:177.

Abeysooriya M, Soria M, Kasu MS, Ziemann M (2021). Gene name errors: Lessons not learned. PLOS Computational Biology 17(7):e1008984.

See Also

gene_names(), gene_ids(), geneid2name().

Examples

hs <- read.delim(system.file("extdata", "example_mapping.tsv", package = "genevintage"))
correct_genenames(c("9-Sep", "1-Dec", "TP53"), mapping = hs)
m <- matrix(1:4, nrow = 2, dimnames = list(c("9-Sep", "TP53"), c("s1", "s2")))
correct_genenames(m, mapping = hs)

# release 95 resolves these as SEPT9 and DEC1
correct_genenames(c("9-Sep", "1-Dec", "TP53"), species = "human", release = 95)

# release 116 resolves these as SEPTIN9 and DELEC1
correct_genenames(c("9-Sep", "1-Dec", "TP53"), species = "human", release = 116)

# no release: the newest, so current spellings
correct_genenames(c("9-Sep", "1-Dec"), species = "human")

correct_genenames(c("1-Mar", "MTARC1"), species = "human", release = 116)

Description

Scores every release the index knows for this species, marks infeasible those that could not have produced the input, and ranks the rest by fit. See vignette("how-it-works") for the scoring.

Usage

detect_release(ids, species = NULL)

DetectRelease(ids, species = NULL)

Arguments

Details

Transcript identifiers (ENSMUST..., FBtr...) are scored against a separate transcript index, which covers the commonly quantified species and GENCODE; for another species pass release to transcript2gene().

Value

A data frame of candidate releases, best first, with release, source (ensembl, gencode for GENCODE's primary-assembly gene set, or gencode_all for its scaffold- and patch-inclusive one), assembly, feasible, dist and n_index. Each assembly has its own row within a release. All candidates are returned because adjacent releases can have indistinguishable fingerprints.

Examples

ids <- readLines(system.file("extdata", "example_ids.txt.gz",
  package = "genevintage"
))
head(detect_release(ids), 3)

Description

Matches identifier prefixes to indexed species.

Usage

detect_species(ids)

DetectSpecies(ids)

Arguments

Value

A data frame of candidate species ordered by the share of ids they explain, with columns species, common, division, prefix, scheme and frac. Rows can tie at the same frac: dog breeds and mouse strains share an identifier space. Check for ties when that distinction matters.

Examples

detect_species(c("ENSMUSG00000051951", "ENSMUSG00000089699"))

# the prefix identifies bonobo
detect_species("ENSPPAG00000021109")[1, c("species", "common", "frac")]

Description

Scores each indexed species/release by informative symbol overlap. Common symbols are downweighted and Excel-prone date-like symbols are excluded. Results below the overlap or score threshold have status = "insufficient"; remaining results are "ambiguous" unless the top candidate meets the margin.

Usage

detect_species_names(
  symbols,
  index,
  min_overlap = 20L,
  min_score = 0.25,
  min_margin = 0.05
)

DetectSpeciesNames(
  symbols,
  index,
  min_overlap = 20L,
  min_score = 0.25,
  min_margin = 0.05
)

Arguments

Value

Ranked data frame with species, release, score, overlap, margin, and status.

Examples

hs <- read.delim(system.file("extdata", "example_mapping.tsv", package = "genevintage"))
hs$species <- "homo_sapiens"
hs$release <- "116"
symbols <- c("TP53", "BRCA1", "GAPDH", "ACTB", "XIST", "HBB", "MALAT1", "PTPRC")
detect_species_names(symbols, build_symbol_index(hs), min_overlap = 5)

Description

Takes gene identifiers or gene names and returns their Entrez identifiers, detecting the species the way the rest of the package does. Cross-references are streamed once per species and release, then cached.

Usage

entrez_ids(
  ids,
  species = NULL,
  release = NULL,
  assembly = NULL,
  source = NULL,
  mapping = NULL,
  quiet = FALSE
)

EntrezIDs(
  ids,
  species = NULL,
  release = NULL,
  assembly = NULL,
  source = NULL,
  mapping = NULL,
  quiet = FALSE
)

Arguments

Details

A gene may carry several Entrez identifiers or none. Each row is a pair; entrez is NA where Ensembl records no cross-reference.

Cross-references are published against Ensembl releases. Identifiers dated to a GENCODE release are looked up in the newest indexed Ensembl release for that species to obtain cross-references between stable identifiers.

Value

A data frame of input, id, name and entrez, one row per pair.

See Also

fetch_xrefs(), gene_names().

Examples

entrez_ids(c("ENSG00000141510", "ENSG00000012048"))
entrez_ids(c("TP53", "BRCA1"), species = "human")

Description

Streamed from the Ensembl GTF on first use, then cached, so later calls are offline. Gene versions are read from GTF attributes or identifier suffixes.

Usage

fetch_mapping(
  species,
  release,
  assembly = NULL,
  source = NULL,
  refresh = FALSE
)

FetchMapping(species, release, assembly = NULL, source = NULL, refresh = FALSE)

Arguments

Value

A data frame of id, name, chr, start, end, strand, span, id_version and biotype, suitable as the mapping argument of gene_names(). span is the genomic extent from first to last base; TPM and FPKM require exonic length. See stream_gtf().

Examples

m <- fetch_mapping("yeast", release = 116)
head(m)

# human release 112 ships two assemblies, so one must be named
fetch_mapping("human", release = 112, assembly = "38")

Description

Streamed from Ensembl Compara on first use, then cached, so later calls are offline. Compara is Ensembl's, so release is an Ensembl release even when the identifiers came from GENCODE.

Usage

fetch_orthologs(
  species,
  to,
  release,
  kind = c("protein", "ncrna"),
  refresh = FALSE
)

FetchOrthologs(
  species,
  to,
  release,
  kind = c("protein", "ncrna"),
  refresh = FALSE
)

Arguments

Value

A data frame of id, ortholog_id, homology_type, identity, ortholog_identity, high_confidence.

Examples

# first call per pair streams a Compara file and caches it; then offline
head(fetch_orthologs("human", to = "mouse", release = 116))

Description

Streamed from the annotation's GTF on first use, then cached, so later calls are offline.

Usage

fetch_transcripts(
  species,
  release,
  assembly = NULL,
  source = NULL,
  refresh = FALSE
)

FetchTranscripts(
  species,
  release,
  assembly = NULL,
  source = NULL,
  refresh = FALSE
)

Arguments

Value

A data frame of transcript_id, id and name, as stream_transcripts() returns it.

See Also

transcript2gene() to map a set of transcript identifiers.

Examples

head(fetch_transcripts("chicken", release = 116))

Description

Streams the cross-reference TSV Ensembl publishes for a species and release, keeps the gene-level pairs and caches them, so later calls are offline.

Usage

fetch_xrefs(species, release, db = "entrez", refresh = FALSE)

FetchXrefs(species, release, db = "entrez", refresh = FALSE)

Arguments

Value

A data frame of id and xref, one row per distinct pair.

See Also

entrez_ids() for the lookup this feeds.

Examples

head(fetch_xrefs("yeast", release = 116))

Description

Use this to see what is there before filtering: the vocabulary differs by species and drifts between releases.

Usage

gene_biotypes(
  ids = NULL,
  species = NULL,
  release = NULL,
  assembly = NULL,
  source = NULL,
  mapping = NULL,
  quiet = FALSE
)

GeneBiotypes(
  ids = NULL,
  species = NULL,
  release = NULL,
  assembly = NULL,
  source = NULL,
  mapping = NULL,
  quiet = FALSE
)

Arguments

Value

A data frame of biotype, class and n, commonest first.

See Also

genes_by_biotype(), coding_genes(), noncoding_genes().

Examples

hs <- read.delim(system.file("extdata", "example_mapping.tsv", package = "genevintage"))
gene_biotypes(mapping = hs)

gene_biotypes(species = "human")

Description

Mapping tables and ortholog pairs are streamed once and cached under tools::R_user_dir("genevintage", "cache"), so a species you have used once works offline afterwards. This reports what is cached and removes it.

Usage

gene_cache(clear = FALSE)

GeneCache(clear = FALSE)

Arguments

Details

The location follows R's own convention and can be moved by setting the R_USER_CACHE_DIR environment variable before the package is used.

Interrupted writes leave .rds.tmp files, listed as partial and eligible for removal.

Value

A data frame with one row per cached file (file, kind, species, to, release, bytes, modified), invisibly when clear is not FALSE. to is the second species of an ortholog pair and is NA for a mapping. Zero rows when nothing is cached.

Examples

# a scratch cache, so the example leaves yours alone
old <- Sys.getenv("R_USER_CACHE_DIR")
Sys.setenv(R_USER_CACHE_DIR = tempfile())
gene_cache() # what is cached, and how large
gene_cache(clear = 90) # drop anything untouched for 90 days
gene_cache(clear = TRUE) # drop all of it
Sys.setenv(R_USER_CACHE_DIR = old)

Description

The reverse of gene_names(). Published marker lists and enrichment results carry symbols or Entrez identifiers; count matrices carry Ensembl ones.

Usage

gene_ids(
  x,
  from = c("auto", "name", "entrez"),
  species = NULL,
  release = NULL,
  assembly = NULL,
  source = NULL,
  mapping = NULL,
  quiet = FALSE
)

GeneIDs(
  x,
  from = c("auto", "name", "entrez"),
  species = NULL,
  release = NULL,
  assembly = NULL,
  source = NULL,
  mapping = NULL,
  quiet = FALSE
)

Arguments

Details

Symbols and Entrez identifiers can each match multiple genes, so the table returns every match. Unmatched inputs are retained with id = NA.

Value

A data frame of input, id and name, one row per match.

See Also

gene_names() for the forward direction, entrez_ids().

Examples

hs <- read.delim(system.file("extdata", "example_mapping.tsv", package = "genevintage"))
gene_ids(c("TP53", "BRCA1"), mapping = hs)

gene_ids(c("TP53", "BRCA1"), species = "human")
gene_ids(c("7157", "672"), from = "entrez", species = "human")

Description

Exon-union gene lengths for one species and release

Usage

gene_lengths(
  species,
  release,
  ids = NULL,
  assembly = NULL,
  source = NULL,
  refresh = FALSE
)

GeneLengths(
  species,
  release,
  ids = NULL,
  assembly = NULL,
  source = NULL,
  refresh = FALSE
)

Arguments

Value

Without ids, a data frame of id and length for every gene in the annotation. With ids, a named integer vector the length of ids, NA where nothing matched.

See Also

fetch_mapping() for genomic span, stream_exon_lengths().

Examples

gene_lengths("human", release = 116, ids = c("ENSG00000141510", "TP53"))

Description

Returns one value per input, in the input's order. An identifier with no name in mapping is returned unchanged, so the result is always usable as row labels.

Usage

gene_names(ids, mapping, unique = FALSE, warn = TRUE)

GeneNames(ids, mapping, unique = FALSE, warn = TRUE)

Arguments

Details

Version suffixes are ignored when matching, so ENSG00000141510.16 resolves against an unversioned mapping and the other way round.

Value

A character vector the same length as ids, carrying a mapped attribute: the logical vector of which inputs found a real name.

See Also

fetch_mapping() to obtain mapping for a species and release.

Examples

m <- data.frame(
  id = c("ENSG00000141510", "ENSG00000284733"),
  name = c("TP53", "ENSG00000284733")
) # second has no symbol
gene_names(c("ENSG00000141510.16", "ENSG00000284733", "ENSG00000999999"), m)
#> "TP53" "ENSG00000284733" "ENSG00000999999"

Description

Detects the species from the identifier prefixes, ranks the Ensembl releases consistent with the identifier set, fetches that release's mapping (streamed once, then cached) and converts. Identifiers with no gene name are returned unchanged.

Usage

geneid2name(
  ids,
  species = NULL,
  release = NULL,
  assembly = NULL,
  source = NULL,
  mapping = NULL,
  unique,
  quiet = FALSE,
  row_ids = NULL
)

GeneID2Name(
  ids,
  species = NULL,
  release = NULL,
  assembly = NULL,
  source = NULL,
  mapping = NULL,
  unique,
  quiet = FALSE,
  row_ids = NULL
)

Arguments

Value

If ids is a plain vector: a character vector the same length as ids, carrying mapped, species, source, release and assembly attributes. If ids is a matrix, sparse Matrix or data frame: the same object with only its row names replaced by gene names; dimensions, row order and other attributes are preserved.

See Also

detect_species(), detect_release(), gene_names().

Examples

# an excerpt of human Ensembl 116; drop `mapping` to detect and fetch the real one
hs <- read.delim(system.file("extdata", "example_mapping.tsv", package = "genevintage"))
ids <- c("ENSG00000141510", "ENSG00000284616", "ENSG00000012048")
geneid2name(ids, mapping = hs) # the unnamed lncRNA keeps its id

m <- matrix(1:6, nrow = 3, dimnames = list(ids, c("s1", "s2")))
geneid2name(m, mapping = hs)

geneid2name(ids) # species and release detected, then fetched

Description

Genes of a given biotype, or class of biotypes

Usage

genes_by_biotype(
  biotype,
  ids = NULL,
  species = NULL,
  release = NULL,
  assembly = NULL,
  source = NULL,
  mapping = NULL,
  quiet = FALSE
)

GenesByBiotype(
  biotype,
  ids = NULL,
  species = NULL,
  release = NULL,
  assembly = NULL,
  source = NULL,
  mapping = NULL,
  quiet = FALSE
)

Arguments

Value

A data frame of id, name, chr and biotype, shaped as mito_genes() returns.

See Also

gene_biotypes() to see the vocabulary first.

Examples

hs <- read.delim(system.file("extdata", "example_mapping.tsv", package = "genevintage"))
genes_by_biotype(c("miRNA", "snoRNA"), mapping = hs)
genes_by_biotype("pseudogene", mapping = hs) # a whole class

genes_by_biotype("lncRNA", species = "human")

Description

Which identifier scheme a vector of IDs uses

Usage

guess_scheme(ids, min_purity = 0.5)

GuessScheme(ids, min_purity = 0.5)

Arguments

Value

A list with scheme, purity and the per-scheme fractions.

Examples

guess_scheme(c("ENSG00000141510", "ENSG00000012048"))$scheme
guess_scheme(c("TP53", "BRCA1"))$scheme

# purity is how a mixed vector announces itself
guess_scheme(c("ENSG00000141510", "TP53"))$purity

Description

The set behind a haemoglobin-contamination metric in single-cell work, beside mito_genes() and ribosomal_genes(). Named per clade: HBA1/HBB in human, Hba-a1/Hbb-bs in mouse, hbaa1/hbba1 in zebrafish.

Usage

hemoglobin_genes(
  ids = NULL,
  species = NULL,
  release = NULL,
  assembly = NULL,
  source = NULL,
  mapping = NULL,
  quiet = FALSE
)

HemoglobinGenes(
  ids = NULL,
  species = NULL,
  release = NULL,
  assembly = NULL,
  source = NULL,
  mapping = NULL,
  quiet = FALSE
)

Arguments

Details

Subunit-letter matching excludes HBEGF, HBS1L and HBP1. Requiring protein_coding also excludes haemoglobin pseudogenes such as HBAP1, HBBP1 and HBZP1.

Value

A data frame of id, name, chr and biotype, shaped as mito_genes() returns.

See Also

mito_genes(), ribosomal_genes().

Examples

hs <- read.delim(system.file("extdata", "example_mapping.tsv", package = "genevintage"))
hemoglobin_genes(mapping = hs)

Description

Matches lncRNA biotype spellings across species and releases, including lncRNA, lincRNA, antisense, processed_transcript and ⁠3prime_overlapping_ncrna⁠.

Usage

lncrna_genes(
  ids = NULL,
  species = NULL,
  release = NULL,
  assembly = NULL,
  source = NULL,
  mapping = NULL,
  quiet = FALSE
)

lncRNAGenes(
  ids = NULL,
  species = NULL,
  release = NULL,
  assembly = NULL,
  source = NULL,
  mapping = NULL,
  quiet = FALSE
)

Arguments

Details

Generic ncRNA entries are excluded. If the annotation contains them and the subset has no lncRNA matches, a message points to genes_by_biotype("ncRNA").

Value

A data frame of id, name, chr and biotype, shaped as mito_genes() returns.

See Also

noncoding_genes() for every non-coding class, gene_biotypes().

Examples

hs <- read.delim(system.file("extdata", "example_mapping.tsv", package = "genevintage"))
lncrna_genes(mapping = hs)

nrow(lncrna_genes(species = "human"))
table(lncrna_genes(species = "zebrafish")$biotype) # antisense and lincRNA

Description

The MHC, which human calls HLA. Every clade names it differently: HLA-A in human, H2-K1 in mouse, mhc1uba in zebrafish, so matching "^HLA-" finds nothing outside primates.

Usage

mhc_genes(
  ids = NULL,
  species = NULL,
  release = NULL,
  assembly = NULL,
  source = NULL,
  mapping = NULL,
  quiet = FALSE
)

MHCGenes(
  ids = NULL,
  species = NULL,
  release = NULL,
  assembly = NULL,
  source = NULL,
  mapping = NULL,
  quiet = FALSE
)

Arguments

Details

Requires protein_coding and an MHC family name pattern. The patterns exclude regional genes such as B2M, TAP1, TAP2 and MICA. Annotations without matching genes return an empty result.

Value

A data frame of id, name, chr and biotype, shaped as mito_genes() returns.

See Also

genes_by_biotype() for the immunoglobulin and T-cell receptor segments, which are a different question.

Examples

hs <- read.delim(system.file("extdata", "example_mapping.tsv", package = "genevintage"))
mhc_genes(mapping = hs)

mhc_genes(species = "human") # coding HLA genes
mhc_genes(species = "mouse") # H2-K1, H2-D1, H2-Aa, ...

Description

Selects genes by mitochondrial sequence names in the annotation for use in mitochondrial count fractions. Sequence-name matching supports the naming conventions of different species.

Usage

mito_genes(
  ids = NULL,
  species = NULL,
  release = NULL,
  assembly = NULL,
  source = NULL,
  mapping = NULL,
  quiet = FALSE
)

MitoGenes(
  ids = NULL,
  species = NULL,
  release = NULL,
  assembly = NULL,
  source = NULL,
  mapping = NULL,
  quiet = FALSE
)

Arguments

Value

A data frame of id, name, chr and biotype, one row per mitochondrial gene. When ids were given, an input column comes first holding the caller's own token, identifier or gene name as passed, so rownames(m) %in% mito_genes(rownames(m))$input subsets a matrix directly whichever kind its row names are.

See Also

sex_genes() for the sex chromosomes.

Examples

hs <- read.delim(system.file("extdata", "example_mapping.tsv", package = "genevintage"))
counts <- matrix(1:72, ncol = 2, dimnames = list(hs$id, c("s1", "s2")))
mito_genes(mapping = hs)
mt <- mito_genes(rownames(counts), mapping = hs)
colSums(counts[mt$input, ]) / colSums(counts) # the mitochondrial fraction

mito_genes(species = "human") # the mitochondrial genes

Description

Genes transcribing functional RNA: lncRNA, miRNA, snRNA, snoRNA, rRNA and the rest. Pseudogenes are a separate class; ask for "pseudogene" through genes_by_biotype() when you want them.

Usage

noncoding_genes(
  ids = NULL,
  species = NULL,
  release = NULL,
  assembly = NULL,
  source = NULL,
  mapping = NULL,
  quiet = FALSE
)

NoncodingGenes(
  ids = NULL,
  species = NULL,
  release = NULL,
  assembly = NULL,
  source = NULL,
  mapping = NULL,
  quiet = FALSE
)

Arguments

Value

A data frame of id, name, chr and biotype.

See Also

coding_genes(), genes_by_biotype().

Examples

hs <- read.delim(system.file("extdata", "example_mapping.tsv", package = "genevintage"))
table(noncoding_genes(mapping = hs)$biotype)

Description

Lists the species with Compara files for a release and division so callers can check availability before streaming a pair.

Usage

ortholog_species(release, division = "vertebrates")

OrthologSpecies(release, division = "vertebrates")

Arguments

Value

A character vector of species names.

Examples

"mus_musculus" %in% ortholog_species(116)

Description

Detects the species from identifiers and defaults to its newest indexed Ensembl release. Fetches that release's Compara orthologs against to (streamed once, then cached) and returns the orthologous identifiers with their gene names.

Usage

orthologs(
  ids,
  to,
  species = NULL,
  release = NULL,
  one2one = TRUE,
  names = TRUE,
  kind = c("protein", "ncrna"),
  quiet = FALSE
)

Orthologs(
  ids,
  to,
  species = NULL,
  release = NULL,
  one2one = TRUE,
  names = TRUE,
  kind = c("protein", "ncrna"),
  quiet = FALSE
)

Arguments

Details

A gene can have several orthologs or none. With one2one = TRUE (the default) only one-to-one orthologs are returned, so there is at most one row per input identifier and the result can be used directly as a lookup. Set it to FALSE to see one-to-many and many-to-many relationships as well.

Value

A data frame with one row per ortholog relationship: id and name for the query gene, ortholog_id and ortholog_name for its counterpart in to (the two name columns when names), then homology_type, identity, ortholog_identity and high_confidence. Identifiers with no ortholog in to are absent, so the result is usually shorter than ids.

See Also

geneid2name() for names within one species.

Examples

orthologs(c("ENSG00000141510", "ENSG00000012048"), to = "mus_musculus")

Description

Handles unversioned and versioned IDs in one vector, ⁠_PAR_Y⁠-style tags, and non-Ensembl input (returned as NA rows).

Usage

parse_ens(x)

ParseEns(x)

Arguments

Value

A data frame with one row per input: id, prefix, feature, num, id_version, tag.

Examples

parse_ens(c(
  "ENSG00000141510.16", "ENSMUSG00000059552",
  "ENSG00000182378.14_PAR_Y", "TP53"
))

Description

Identifier numbers are assigned upward, so qmax should not fall as releases advance within one species and assembly. Ensembl retires genes at the top of the range occasionally, so only a fall of more than 1% is reported. Only numerically ordered schemes are checked.

Usage

qmax_violations(fp = .fp())

QmaxViolations(fp = .fp())

Arguments

Value

A character vector of violation messages, empty when the index is sound.

Examples

# report ordering violations in the shipped index
qmax_violations()

Description

Accepts the Ensembl name ("homo_sapiens"), the scientific name ("Homo sapiens"), Ensembl's display name ("Zebrafish", "Giant panda") or a common shorthand ("human", "mouse", "rat", "fly", "yeast"). Matching ignores case, punctuation and underscores.

Usage

resolve_species(x, quiet = FALSE)

ResolveSpecies(x, quiet = FALSE)

Arguments

Details

An unambiguous partial match is accepted and reported; an ambiguous one is refused with the candidates. The "mouse" alias selects mus_musculus even when strain genomes also match the word.

Value

The Ensembl species name, e.g. "homo_sapiens".

Examples

resolve_species("human")
resolve_species("Zebrafish")

Description

which selects the ribosomal set:

Usage

ribosomal_genes(
  ids = NULL,
  which = c("protein", "rrna", "mito", "all"),
  species = NULL,
  release = NULL,
  assembly = NULL,
  source = NULL,
  mapping = NULL,
  quiet = FALSE
)

RibosomalGenes(
  ids = NULL,
  which = c("protein", "rrna", "mito", "all"),
  species = NULL,
  release = NULL,
  assembly = NULL,
  source = NULL,
  mapping = NULL,
  quiet = FALSE
)

Arguments

Details

• "protein" (the default): the genes encoding the ribosome's proteins, the set behind a single-cell ribosomal-content metric.

• "rrna": the RNA components, by biotype (rRNA and Mt_rRNA).

• "mito": the mitoribosome's proteins, named with an M prefix. These are nuclear genes; mito_genes() does not return them.

• "all": every one of the above.

The "^RP[SL]" symbol pattern is restricted to protein_coding genes to exclude pseudogenes and lncRNAs. A name rule also excludes S6 kinases (RPS6KA1 to RPS6KL1) and RPS19BP1.

Value

A data frame of id, name, chr and biotype, shaped as mito_genes() returns.

See Also

mito_genes(), genes_by_biotype().

Examples

hs <- read.delim(system.file("extdata", "example_mapping.tsv", package = "genevintage"))
counts <- matrix(1:72, ncol = 2, dimnames = list(hs$id, c("s1", "s2")))
rb <- ribosomal_genes(rownames(counts), mapping = hs)
colSums(counts[rb$input, ]) / colSums(counts) # ribosomal content
ribosomal_genes(mapping = hs, which = "rrna")

ribosomal_genes(species = "human", which = "rrna")

Description

The RNA components of the ribosome, by biotype: rRNA in the nucleus and Mt_rRNA in the mitochondrion.

Usage

rrna_genes(
  ids = NULL,
  species = NULL,
  release = NULL,
  assembly = NULL,
  source = NULL,
  mapping = NULL,
  quiet = FALSE
)

rRNAGenes(
  ids = NULL,
  species = NULL,
  release = NULL,
  assembly = NULL,
  source = NULL,
  mapping = NULL,
  quiet = FALSE
)

Arguments

Details

rRNA_pseudogene belongs with the pseudogenes. Ask for it with genes_by_biotype("rRNA_pseudogene").

Value

A data frame of id, name, chr and biotype, shaped as mito_genes() returns.

See Also

ribosomal_genes() for the ribosome's proteins, trna_genes().

Examples

hs <- read.delim(system.file("extdata", "example_mapping.tsv", package = "genevintage"))
rrna_genes(mapping = hs)

rrna_genes(species = "human")

Description

Sex chromosome names vary by clade: mammals use X and Y, birds Z and W, and C. elegans X. Annotations without recognised sex chromosomes return no rows.

Usage

sex_genes(
  ids = NULL,
  which = NULL,
  species = NULL,
  release = NULL,
  assembly = NULL,
  source = NULL,
  mapping = NULL,
  quiet = FALSE
)

SexGenes(
  ids = NULL,
  which = NULL,
  species = NULL,
  release = NULL,
  assembly = NULL,
  source = NULL,
  mapping = NULL,
  quiet = FALSE
)

Arguments

Value

A data frame of id, name, chr and biotype, one row per gene, shaped as mito_genes() returns.

See Also

mito_genes().

Examples

hs <- read.delim(system.file("extdata", "example_mapping.tsv", package = "genevintage"))
sex_genes(mapping = hs, which = "Y")

sex_genes(species = "human", which = "Y") # Y-linked genes

Description

Species the index covers, with their common names

Usage

species_table(pattern = NULL)

SpeciesTable(pattern = NULL)

Arguments

Value

A data frame of species, common, taxonomy_id and division.

Examples

head(species_table("mouse"))

Description

Keeps only exon lines. Gene ids are read from the gene_id attribute, so a GENCODE GTF yields versioned ids, as its gene lines do in stream_gtf().

Usage

stream_exon_lengths(url, chunk = 1e+05)

StreamExonLengths(url, chunk = 1e+05)

Arguments

Value

A data frame of id and length (bases).

Examples

stream_exon_lengths(paste0(
  "https://ftp.ensembl.org/pub/release-116/gtf/",
  "saccharomyces_cerevisiae/",
  "Saccharomyces_cerevisiae.R64-1-1.63.gtf.gz"
))

Description

Decompresses the stream in chunks and retains gene lines. If there are none, reads the first record per gene from the remaining feature lines.

Usage

stream_gtf(url, chunk = 1e+05)

StreamGTF(url, chunk = 1e+05)

Arguments

Value

A data frame of id, name, chr, start, end, strand, span, id_version and biotype. span is the genomic extent from first to last base; TPM and FPKM require exonic length.

Examples

# any Ensembl-shaped GTF; nothing is written to disk
stream_gtf(paste0(
  "https://ftp.ensembl.org/pub/release-116/gtf/",
  "saccharomyces_cerevisiae/",
  "Saccharomyces_cerevisiae.R64-1-1.63.gtf.gz"
))

Description

Filters the Compara stream in chunks to retain orthologs for the requested target species, limiting memory to the selected pair.

Usage

stream_homologies(url, to, swap = FALSE, chunk = 2e+05)

StreamHomologies(url, to, swap = FALSE, chunk = 2e+05)

Arguments

Value

A data frame of id, ortholog_id, homology_type, identity, ortholog_identity, high_confidence.

Examples

url <- paste0(
  "https://ftp.ensembl.org/pub/release-116/tsv/ensembl-compara/",
  "homologies/mus_musculus/",
  "Compara.116.protein_default.homologies.tsv.gz"
)
head(stream_homologies(url, to = "homo_sapiens"))

Description

Keeps transcript lines. GTFs before Ensembl release 75 have none, so a chunk without them is read from its exon and CDS lines, which carry the same transcript_id, gene_id and gene_name; duplicates are dropped.

Usage

stream_transcripts(url, chunk = 1e+05)

StreamTranscripts(url, chunk = 1e+05)

Arguments

Value

A data frame of transcript_id, id (the gene) and name (the gene name, NA where the annotation gives none). Identifiers keep whatever version suffix the GTF writes: GENCODE versions them, Ensembl does not.

See Also

fetch_transcripts() for the cached table of one release.

Examples

stream_transcripts(paste0(
  "https://ftp.ensembl.org/pub/release-116/gtf/",
  "saccharomyces_cerevisiae/",
  "Saccharomyces_cerevisiae.R64-1-1.63.gtf.gz"
))

Description

Deduplicate gene-level pairs from transcript rows while streaming to limit memory to distinct pairs.

Usage

stream_xrefs(url, db = "EntrezGene", chunk = 2e+05)

StreamXrefs(url, db = "EntrezGene", chunk = 2e+05)

Arguments

Value

A data frame of id and xref.

Examples

stream_xrefs(paste0(
  "https://ftp.ensembl.org/pub/release-116/tsv/saccharomyces_cerevisiae/",
  "Saccharomyces_cerevisiae.R64-1-1.63.entrez.tsv.gz"
))

Description

Detects the species from the identifier prefix (ENSMUST, ENSGALT, ...), fetches the annotation's transcript table (streamed once, then cached) and returns each transcript's gene identifier and gene name. Version suffixes are ignored when matching, so ENSMUST00000178537.2 resolves against an unversioned annotation and the other way round.

Usage

transcript2gene(
  ids,
  species = NULL,
  release = NULL,
  assembly = NULL,
  source = NULL,
  mapping = NULL,
  quiet = FALSE
)

Transcript2Gene(
  ids,
  species = NULL,
  release = NULL,
  assembly = NULL,
  source = NULL,
  mapping = NULL,
  quiet = FALSE
)

Arguments

Details

Without release, detect_release() dates the transcript identifiers against a transcript fingerprint index of Ensembl and GENCODE for the commonly quantified species. source and assembly narrow the candidates.

When the best-scoring release leaves any id unmapped, the best release of each other annotation family (Ensembl, GENCODE, GENCODE ALL) is fetched too and the best-covering one kept: a filtered transcriptome (cDNA only) dates by its newest id but leaves its family open.

A species outside that index, a set too small to date (a handful of ids), or dated releases explaining less than 90% of the input fall back to coverage: the newest Ensembl release of each assembly is tried, newest first, and the best-covering one kept. Chicken needs this: GRCg7b (release 107 on) renumbered every identifier, so GRCg6a transcripts only map at release 106 or earlier.

Value

A data frame with one row per input, in order: input, transcript_id (as the annotation writes it), gene_id and gene_name. Unmapped inputs have NA in the last three. A gene without a name has its identifier as gene_name. Attributes species, source, release and assembly record the annotation used.

See Also

aggregate_transcripts() to sum a transcript-level matrix to genes.

Examples

tx <- data.frame(
  transcript_id = c("ENST00000269305", "ENST00000357654"),
  id = c("ENSG00000141510", "ENSG00000012048"), name = c("TP53", "BRCA1")
)
transcript2gene(c("ENST00000269305.9", "ENST00000357654.9"), mapping = tx)

transcript2gene(c("ENSMUST00000178537.2", "ENSMUST00000178862.2"))
transcript2gene(c("ENSGALT00000000003", "ENSGALT00000000004"))

Description

Ensembl names them Mt_tRNA on the mitochondrial chromosome and tRNA in the nucleus. Which of those an annotation actually contains varies: the vertebrate GTFs carry only the mitochondrial tRNAs, since nuclear tRNA genes are predicted separately and lie outside the gene set. Invertebrate, fungal and plant annotations include the nuclear ones. The chr and biotype columns say which kind each row is.

Usage

trna_genes(
  ids = NULL,
  species = NULL,
  release = NULL,
  assembly = NULL,
  source = NULL,
  mapping = NULL,
  quiet = FALSE
)

tRNAGenes(
  ids = NULL,
  species = NULL,
  release = NULL,
  assembly = NULL,
  source = NULL,
  mapping = NULL,
  quiet = FALSE
)

Arguments

Value

A data frame of id, name, chr and biotype, shaped as mito_genes() returns.

See Also

ribosomal_genes(), genes_by_biotype().

Examples

hs <- read.delim(system.file("extdata", "example_mapping.tsv", package = "genevintage"))
trna_genes(mapping = hs)

trna_genes(species = "human") # the mitochondrial tRNAs
table(trna_genes(species = "yeast")$chr) # nuclear, by chromosome