Read .idat files

Read .idat files

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

if (FALSE) {
read_idats('9976861004_R01C01')
}