deidentify: De-identify IDATs by removing SNP probes

Description Usage Arguments Value Examples

Description

Mask SNP probe intensity mean by zero.

Usage

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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

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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.