readTranscriptFeatures-methods: Function for reading exon intron and promoter structure from...

Description Usage Arguments Value Note Examples

Description

Function for reading exon intron and promoter structure from a given bed file

Usage

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readTranscriptFeatures(location,remove.unusual=TRUE,
                              up.flank=1000,down.flank=1000,unique.prom=TRUE)

## S4 method for signature 'character'
readTranscriptFeatures(location, remove.unusual = TRUE,
  up.flank = 1000, down.flank = 1000, unique.prom = TRUE)

Arguments

location

location of the bed file with 12 or more columns. The file can end in .gz, .bz2, .xz, or .zip and/or start with http:// or ftp://. If the file is not compressed it can also start with https:// or ftps://.

remove.unusual

remove the chromomesomes with unsual names, mainly random chromsomes etc

up.flank

up-stream from TSS to detect promoter boundaries

down.flank

down-stream from TSS to detect promoter boundaries

unique.prom

get only the unique promoters, promoter boundaries will not have a gene name if you set this option to be TRUE

Value

a GRangesList containing locations of exon/intron/promoter/TSS

Note

one bed track per file is only accepted, the bed files with multiple tracks will cause en error

Examples

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my.bed12.file = system.file("extdata/chr21.refseq.hg19.bed", package = "genomation")
my.bed12.file
feats = readTranscriptFeatures(my.bed12.file) 
names(feats)
sapply(feats, head)

BIMSBbioinfo/genomation documentation built on Feb. 4, 2018, 12:11 p.m.