importSJ: Import STAR Splice Junctions

Description Usage Arguments Details Value Author(s) Examples

View source: R/importSJ.R

Description

Import the SJ.out.tab files produced by STAR

Usage

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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

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

Value

A tibble

Author(s)

Stephen Pederson <stephen.pederson@adelaide.edu.au>

Examples

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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)

UofABioinformaticsHub/fastqcReports documentation built on Nov. 21, 2020, 7:44 p.m.