loadSTAR_chimeric: loadSTAR_chimeric

Description Usage Arguments Details

View source: R/file_io.R

Description

Loads chimeric output file from the STAR aligner and returns a list containing three items (a data table, alignment stats and command line).

Usage

1
loadSTAR_chimeric(filename = NULL, ID_index = 0, returnColIdx = 1:21)

Arguments

filename

: filename of the STAR chimeric output file. Can be gzipped

ID_index

: An index (single integer) which will be added as a separate column in the returned data table. Useful when collating multiple files into one large matrix like object.

returnColIdx

: Numeric index of columns to return. Default 1:15

Details

:

Reads in a text or gzipped chimeric output file generated by the STAR aligner. Function automatically detects if the last two lines contains meta-data (produced from STAR 2.7) onwards.

Returns a list of containing three items: (1) data_set (2) alignmentStats and (3) commandLine.

The column names of data_set are defined as c("chromDonor","startDonor","strandDonor", "chromAcceptor", "startAcceptor","strandAcceptor","JuncType", "RepeatLength_L", "RepeatLength_R", "ReadName","FirstBase_1stSeq","CIGAR_1stSeg", "FirstBase_2ndSeq","CIGAR_2ndSeg", "Multimapping")

If ID_index is set to a value greater than 0 then an additional column called "DataSet" is created.

Columns can be subsetted by defining returnColIdx with an integer value that correspond to order of column names listed above.


VCCRI/Ularcirc documentation built on July 3, 2020, 9:57 a.m.