extractSpliceEvents

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Description

Extracts the location of target, upstream and downstream splice sites Used for calculations and genome visualizations Adds 1bp to 0base start (MATS format)

Usage

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extractSpliceEvents(data = NULL, filetype = "mats", splicetype = "SE",
  fdr = 1, inclusion = 1)

Arguments

data

character. path to file

filetype

character. type of splicing output. c('mats','custom'). see Details.

splicetype

character. c('SE', 'RI', 'MXE', 'A5SS', 'A3SS')

fdr

numeric. false discovery rate filter range [0,1]

inclusion

numeric. splicing inclusion range, takes absolute value

Details

filetype 'custom' should provide a 9-column tab-delimited text file with the following columns: GeneID (Ensembl gene id), chr, strand, exonStart, exonEnd, upstreamES, upstreamEE, downstreamES, downstreamEE eg. ENSG0000012345 chr1 + 3 4 1 2 5 6

for filetype 'custom', coordinates are expected to be in base-1.

Value

list containing information on
(1) original file type
(2) splice event type
(3) data.frame with splicing regions

Author(s)

Diana Low

See Also

http://rnaseq-mats.sourceforge.net/user_guide.htm for MATS file definition

Examples

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data_path<-system.file("extdata",package="SPLINTER")
splice_data<-extractSpliceEvents(data=paste(data_path,"/skipped_exons.txt",sep=""))