Read .idat files
read_idats.Rd
Read .idat files
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