findLibrariesInFolder {ORFik} | R Documentation

## 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", "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.

[Package ORFik version 1.14.7 Index]