searchIDATprefixes: Identify IDATs from a directory

In sesame: Tools For Analyzing Illumina Infinium DNA Methylation Arrays

Description

The input is the directory name as a string. The function identifies all the IDAT files under the directory. The function returns a vector of such IDAT prefixes under the directory.

Usage

searchIDATprefixes(dir.name, recursive = TRUE, use.basename = TRUE)

Arguments

dir.name	the directory containing the IDAT files.
recursive	search IDAT files recursively
use.basename	basename of each IDAT path is used as sample name This won't work in rare situation where there are duplicate IDAT files.

Value

the IDAT prefixes (a vector of character strings).

Examples

## only search what are directly under
IDATprefixes <- searchIDATprefixes(
    system.file("extdata", "", package = "sesameData"))

## search files recursively is by default
IDATprefixes <- searchIDATprefixes(
    system.file(package = "sesameData"), recursive=TRUE)

sesame documentation built on Nov. 15, 2020, 2:08 a.m.