importSJ {ngsReports} | R Documentation

## Import STAR Splice Junctions

### Description

Import the SJ.out.tab files produced by STAR

### Usage

    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

    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)

[Package ngsReports version 1.8.1 Index]