deidentify: De-identify IDATs by removing SNP probes
In zwdzwd/sesame: SEnsible Step-wise Analysis of DNA MEthylation BeadChips

deIdentify

R Documentation

De-identify IDATs by removing SNP probes

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)

zwdzwd/sesame documentation built on Dec. 21, 2024, 1:20 p.m.