rawFiles | R Documentation |
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"
)
datadir |
The main directory where each of the |
sampledirs |
A character vector with the names of the sample
directories. If |
samplepatt |
If specified and |
fileterm |
Name of the BAM or BigWig file used in each sample. By
default it is set to |
This function can also be used to identify a set of BigWig files.
A vector with the full paths to the raw files and sample names stored as the vector names.
Leonardo Collado-Torres
loadCoverage
## 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
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