findLibrariesInFolder: Get all library files in folder/folders of given types

In JokingHero/ORFik: Open Reading Frames in Genomics

Get all library files in folder/folders of given types

Description

Will try to guess paired / unpaired wig, bed, bam files.

Usage

findLibrariesInFolder(dir, types, pairedEndBam = FALSE)

Arguments

dir	Which directory / directories to create experiment from, must be a directory with NGS data from your experiment. Will include all files of file type specified by "types" argument. So do not mix files from other experiments in the same folder!
types	Default c("bam", "bed", "wig", "bigWig","ofst"), which types of libraries to allow as NGS data.
pairedEndBam	logical FALSE, else TRUE, or a logical list of TRUE/FALSE per library you see will be included (run first without and check what order the files will come in) 1 paired end file, then two single will be c(T, F, F). If you have a SRA metadata csv file, you can set this argument to study$LibraryLayout == "PAIRED", where study is the SRA metadata for all files that was aligned.

Details

Set pairedEndBam if you have paired end reads as a single bam file.

Value

(data.table) All files found from types parameter. With 2 extra column (logical), is it wig pairs, and paired bam files.

JokingHero/ORFik documentation built on Dec. 21, 2024, 12:01 a.m.