deidentify: De-identify IDATs by removing SNP probes

In sesame: Tools For Analyzing Illumina Infinium DNA Methylation Arrays

Description

Mask SNP probe intensity mean by zero.

Usage

deIdentify(path, out_path = NULL, snps = NULL, mft = NULL, randomize = FALSE)

Arguments

path	input IDAT file
out_path	output IDAT file
snps	SNP definition, if not given, default to SNP probes
mft	sesame-compatible manifest if non-standard
randomize	whether to randomize the SNPs. if TRUE, randomize the signal intensities. one can use set.seed to reidentify the IDAT with the secret seed (see examples). If FALSE, this sets all SNP intensities to zero.

Value

NULL, changes made to the IDAT files

Examples

my_secret <- 13412084
set.seed(my_secret)
temp_out <- tempfile("test")
deIdentify(system.file(
    "extdata", "4207113116_A_Grn.idat", package = "sesameData"),
     temp_out, randomize = TRUE)
unlink(temp_out)

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