extractSpliceEvents: extractSpliceEvents

Description Usage Arguments Details Value Author(s) See Also Examples

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

1
2
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

1
2
data_path<-system.file("extdata",package="SPLINTER")
splice_data<-extractSpliceEvents(data=paste(data_path,"/skipped_exons.txt",sep=""))


Search within the SPLINTER package
Search all R packages, documentation and source code

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.