EnsDb-lengths: Calculating lengths of features

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

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.v75)
edb <- EnsDb.Hsapiens.v75

#####    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)

YTLogos/ensembldb documentation built on May 3, 2019, 9:03 p.m.