Import STAR Splice Junctions

Import the SJ.out.tab files produced by STAR

importSJ(x, stripPaths = TRUE)

Arguments

x

vector of file paths to SJ.out.tab files

stripPaths

logical(1) Remove directory prefixes from the file paths in x

Value

A tibble

Details

Imports one or more splice-junction output files as produced by STAR. If all are located in separated directories with identical names, be sure to set the argument stripPaths = FALSE

All co-ordinates are 1-based, in keeping with the STAR manual

Author

Stephen Pederson stephen.pederson@adelaide.edu.au

Examples

sjFiles <- system.file("extdata", "SJ.out.tab", package = "ngsReports")
# Import leaving the complete file path in the column Filename
# The argument srtipPaths is set as TRUE by default
df <- importSJ(sjFiles, stripPaths = FALSE)