read_idats: Read .idat files

In hhhh5/ewastools: EWAS Tools

Read .idat files

Description

Read .idat files

Usage

read_idats(idat_files, quiet = FALSE)

Arguments

idat_files	Character vector of relative or absolute filepaths, but without the suffixes '_Grn.idat' and '_Red.idat'. IDATs for red and green channel must have the same prefix and be stored in the same folder. E.g., a sample with the idats 200607110235_R01C01_Red.idat and 200607110235_R01C01_Grn.idat would be passed to read_idats as "200607110235_R01C01".
quiet	If TRUE, suppresses the progress bar (useful for RMarkdown scripts).

Value

A list containing

manifest	A data.table describing the probes
M	intensities of targeting methylated sequences
U	intensities of targeting unmethylated sequences
N	number of beads from which average intensities in M were derived
V	number of beads from which average intensities in U were derived
ctrlG	Intensities of the control probes in the green color channel
ctrlR	Intensities of the control probes in the red color channel
meta	A data.table containing unique sample_ids and metadata

Examples

## Not run: 
read_idats('9976861004_R01C01')

## End(Not run)

hhhh5/ewastools documentation built on Feb. 7, 2024, 6:21 p.m.