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

In ORFik: Open Reading Frames in Genomics

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
types	Default (bam, bed, wig), which types of libraries to allow
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.

ORFik documentation built on March 27, 2021, 6 p.m.