scan_directory: Scan a directory for IDAT files.

In cgeisenberger/crystalmeth: Streamlined Methylation-Based Classification of Tumors

Description

scan_directory scans a directory, detects IDAT and non-IDAT files and reports basenames for complete cases .

Usage

scan_directory(dir)

Arguments

dir	Directory to scan.

Details

This function scans a directory. Its main purpose is to identify cases with paired (_Grn.idat and _Red.idat) IDAT files. It will also report any invalid files (types other than .idat) or cases where one of the input files is missing.

Note: Will report basenames, not filenames for IDAT files

Use accessor functions get_all, get_invalid, get_cases, get_green_only and get_red_only to extract data.

This implementation might currently be overkill, but was created with forward compatibility in mind (might be replaced by a specialized class in future versions).

Value

Returns a list with the following slots:

all	List of all files in dir
invalid	List of non-IDAT files
green_only	Basenames of cases with missing RED channel data
red_only	Basenames of cases with missing GREEN channel data
cases	Basenames of cases with correctly paired IDAT files

cgeisenberger/crystalmeth documentation built on Aug. 28, 2020, 9:35 a.m.