Construct full paths to a group of raw input files

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.

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.

Value

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

Details

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

See also

loadCoverage

Author

Leonardo Collado-Torres

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
#>                                                   ERR009101_accepted_hits.bam 
#> "/__w/_temp/Library/derfinder/extdata/genomeData/ERR009101_accepted_hits.bam" 
#>                                                   ERR009102_accepted_hits.bam 
#> "/__w/_temp/Library/derfinder/extdata/genomeData/ERR009102_accepted_hits.bam" 
#>                                                   ERR009105_accepted_hits.bam 
#> "/__w/_temp/Library/derfinder/extdata/genomeData/ERR009105_accepted_hits.bam" 
#>                                                   ERR009107_accepted_hits.bam 
#> "/__w/_temp/Library/derfinder/extdata/genomeData/ERR009107_accepted_hits.bam" 
#>                                                   ERR009108_accepted_hits.bam 
#> "/__w/_temp/Library/derfinder/extdata/genomeData/ERR009108_accepted_hits.bam" 
#>                                                   ERR009112_accepted_hits.bam 
#> "/__w/_temp/Library/derfinder/extdata/genomeData/ERR009112_accepted_hits.bam" 
#>                                                   ERR009115_accepted_hits.bam 
#> "/__w/_temp/Library/derfinder/extdata/genomeData/ERR009115_accepted_hits.bam" 
#>                                                   ERR009116_accepted_hits.bam 
#> "/__w/_temp/Library/derfinder/extdata/genomeData/ERR009116_accepted_hits.bam" 
#>                                                   ERR009131_accepted_hits.bam 
#> "/__w/_temp/Library/derfinder/extdata/genomeData/ERR009131_accepted_hits.bam" 
#>                                                   ERR009138_accepted_hits.bam 
#> "/__w/_temp/Library/derfinder/extdata/genomeData/ERR009138_accepted_hits.bam" 
#>                                                   ERR009144_accepted_hits.bam 
#> "/__w/_temp/Library/derfinder/extdata/genomeData/ERR009144_accepted_hits.bam" 
#>                                                   ERR009145_accepted_hits.bam 
#> "/__w/_temp/Library/derfinder/extdata/genomeData/ERR009145_accepted_hits.bam" 
#>                                                   ERR009148_accepted_hits.bam 
#> "/__w/_temp/Library/derfinder/extdata/genomeData/ERR009148_accepted_hits.bam" 
#>                                                   ERR009151_accepted_hits.bam 
#> "/__w/_temp/Library/derfinder/extdata/genomeData/ERR009151_accepted_hits.bam" 
#>                                                   ERR009152_accepted_hits.bam 
#> "/__w/_temp/Library/derfinder/extdata/genomeData/ERR009152_accepted_hits.bam" 
#>                                                   ERR009153_accepted_hits.bam 
#> "/__w/_temp/Library/derfinder/extdata/genomeData/ERR009153_accepted_hits.bam" 
#>                                                   ERR009159_accepted_hits.bam 
#> "/__w/_temp/Library/derfinder/extdata/genomeData/ERR009159_accepted_hits.bam" 
#>                                                   ERR009161_accepted_hits.bam 
#> "/__w/_temp/Library/derfinder/extdata/genomeData/ERR009161_accepted_hits.bam" 
#>                                                   ERR009163_accepted_hits.bam 
#> "/__w/_temp/Library/derfinder/extdata/genomeData/ERR009163_accepted_hits.bam" 
#>                                                   ERR009164_accepted_hits.bam 
#> "/__w/_temp/Library/derfinder/extdata/genomeData/ERR009164_accepted_hits.bam" 
#>                                                   ERR009167_accepted_hits.bam 
#> "/__w/_temp/Library/derfinder/extdata/genomeData/ERR009167_accepted_hits.bam" 
#>                                                   SRR031812_accepted_hits.bam 
#> "/__w/_temp/Library/derfinder/extdata/genomeData/SRR031812_accepted_hits.bam" 
#>                                                   SRR031835_accepted_hits.bam 
#> "/__w/_temp/Library/derfinder/extdata/genomeData/SRR031835_accepted_hits.bam" 
#>                                                   SRR031867_accepted_hits.bam 
#> "/__w/_temp/Library/derfinder/extdata/genomeData/SRR031867_accepted_hits.bam" 
#>                                                   SRR031868_accepted_hits.bam 
#> "/__w/_temp/Library/derfinder/extdata/genomeData/SRR031868_accepted_hits.bam" 
#>                                                   SRR031900_accepted_hits.bam 
#> "/__w/_temp/Library/derfinder/extdata/genomeData/SRR031900_accepted_hits.bam" 
#>                                                   SRR031904_accepted_hits.bam 
#> "/__w/_temp/Library/derfinder/extdata/genomeData/SRR031904_accepted_hits.bam" 
#>                                                   SRR031914_accepted_hits.bam 
#> "/__w/_temp/Library/derfinder/extdata/genomeData/SRR031914_accepted_hits.bam" 
#>                                                   SRR031936_accepted_hits.bam 
#> "/__w/_temp/Library/derfinder/extdata/genomeData/SRR031936_accepted_hits.bam" 
#>                                                   SRR031958_accepted_hits.bam 
#> "/__w/_temp/Library/derfinder/extdata/genomeData/SRR031958_accepted_hits.bam" 
#>                                                   SRR031960_accepted_hits.bam 
#> "/__w/_temp/Library/derfinder/extdata/genomeData/SRR031960_accepted_hits.bam"