rawFiles: Construct full paths to a group of raw input files

In lcolladotor/derfinder: Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach

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

lcolladotor/derfinder documentation built on Dec. 17, 2024, 4:53 p.m.