EnsDb-lengths: Calculating lengths of features

In jorainer/ensembldb: Utilities to create and use Ensembl-based annotation databases

Calculating lengths of features

Description

These methods allow to calculate the lengths of features (transcripts, genes, CDS, 3' or 5' UTRs) defined in an EnsDb object or database.

Usage

## S4 method for signature 'EnsDb'
lengthOf(x, of="gene", filter = AnnotationFilterList())

Arguments

(In alphabetic order)

filter	A filter describing which results to retrieve from the database. Can be a single object extending AnnotationFilter, an AnnotationFilterList object combining several such objects or a formula representing a filter expression (see examples below or AnnotationFilter for more details).
of	for lengthOf: whether the length of genes or transcripts should be retrieved from the database.
x	For lengthOf: either an EnsDb or a GRangesList object. For all other methods an EnsDb instance.

Value

For lengthOf: see method description above.

Methods and Functions

lengthOf

Retrieve the length of genes or transcripts from the database. The length is the sum of the lengths of all exons of a transcript or a gene. In the latter case the exons are first reduced so that the length corresponds to the part of the genomic sequence covered by the exons.

Note: in addition to this method, also the transcriptLengths function in the GenomicFeatures package can be used.

Author(s)

Johannes Rainer

See Also

exonsBy transcripts transcriptLengths

Examples

library(EnsDb.Hsapiens.v86)
edb <- EnsDb.Hsapiens.v86

#####    lengthOf
##
## length of a specific gene.
lengthOf(edb, filter = GeneIdFilter("ENSG00000000003"))

## length of a transcript
lengthOf(edb, of = "tx", filter = TxIdFilter("ENST00000494424"))

## Average length of all protein coding genes encoded on chromosomes X
mean(lengthOf(edb, of = "gene",
              filter = ~ gene_biotype == "protein_coding" &
                  seq_name == "X"))

## Average length of all snoRNAs
mean(lengthOf(edb, of = "gene",
              filter = ~ gene_biotype == "snoRNA" &
                  seq_name == "X"))

##### transcriptLengths
##
## Calculate the length of transcripts encoded on chromosome Y, including
## length of the CDS, 5' and 3' UTR.
len <- transcriptLengths(edb, with.cds_len = TRUE, with.utr5_len = TRUE,
                         with.utr3_len = TRUE, filter = SeqNameFilter("Y"))
head(len)

jorainer/ensembldb documentation built on Aug. 23, 2024, 1:16 p.m.