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=list())

Arguments

(In alphabetic order)

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=list(GeneidFilter("ENSG00000000003")))

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

## average length of all protein coding genes encoded on chromosomes X
## and Y
mean(lengthOf(edb, of="gene",
              filter=list(GenebiotypeFilter("protein_coding"),
                  SeqnameFilter(c("X", "Y")))))

## average length of all snoRNAs
mean(lengthOf(edb, of="gene",
              filter=list(GenebiotypeFilter("snoRNA"),
                  SeqnameFilter(c("X", "Y")))))

##### 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)

Results

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> library(ensembldb)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: GenomicRanges
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/ensembldb/EnsDb-lengths.Rd_%03d_medium.png", width=480, height=480)
> ### Name: lengthOf
> ### Title: Calculating lengths of features
> ### Aliases: lengthOf lengthOf,GRangesList-method lengthOf,EnsDb-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> 
> library(EnsDb.Hsapiens.v75)
> edb <- EnsDb.Hsapiens.v75
> 
> #####    lengthOf
> ##
> ## length of a specific gene.
> lengthOf(edb,
+          filter=list(GeneidFilter("ENSG00000000003")))
ENSG00000000003 
           2968 
> 
> ## length of a transcript
> lengthOf(edb, of="tx",
+          filter=list(TxidFilter("ENST00000494424")))
ENST00000494424 
            820 
> 
> ## average length of all protein coding genes encoded on chromosomes X
> ## and Y
> mean(lengthOf(edb, of="gene",
+               filter=list(GenebiotypeFilter("protein_coding"),
+                   SeqnameFilter(c("X", "Y")))))
[1] 3715.94
> 
> ## average length of all snoRNAs
> mean(lengthOf(edb, of="gene",
+               filter=list(GenebiotypeFilter("snoRNA"),
+                   SeqnameFilter(c("X", "Y")))))
[1] 119.3333
> 
> ##### 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)
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>