rawFiles {derfinder} | R Documentation

## Construct full paths to a group of raw input files

### Description

For a group of samples this function creates the list of paths to the raw input files which can then be used in loadCoverage. The raw input files are either BAM files or BigWig files.

### Usage

    rawFiles(datadir = NULL, sampledirs = NULL, samplepatt = NULL,
      fileterm = "accepted_hits.bam")

### Arguments

`datadir` | The main directory where each of the `sampledirs` is a sub-directory of `datadir`.
`sampledirs` | A character vector with the names of the sample directories. If `datadir` is `NULL` it is then assumed that `sampledirs` specifies the full path to each sample.
`samplepatt` | If specified and `sampledirs` is set to `NULL`, then the directories matching this pattern in `datadir` (set to `.` if it's set to `NULL`) are used as the sample directories.
`fileterm` | Name of the BAM or BigWig file used in each sample. By default it is set to `accepted_hits.bam` since that is the automatic name generated when aligning with TopHat. If `NULL` it is then ignored when reading the rawfiles. This can be useful if all the raw files are stored in a single directory.

### Details

This function can also be used to identify a set of BigWig files.

### Value

A vector with the full paths to the raw files and sample names stored as the vector names.

### Author(s)

Leonardo Collado-Torres

### See Also

loadCoverage

### Examples

    ## Get list of BAM files included in derfinder
    datadir <- system.file('extdata', 'genomeData', package='derfinder')
    files <- rawFiles(datadir=datadir, samplepatt='*accepted_hits.bam$',
        fileterm=NULL)
    files

[Package derfinder version 1.14.0 Index]