Hi, I am new to methylation analysis. I'm wondering if it's possible to champ.load() all IDAT files from multiple subdirectories. Our methylation data is stored on a server and arranged by samples (each contains a pair of IDAT files, a raw and a normalized .txt file). Moving thousands of IDAT files out to the parent folder seems to create a mess. So, I really want to make sure if there is any other solution before I ask my school CIO for further permission to move the files. I hope this isn't a duplicate question. Thank you!

It may be technically difficult to use champ.load() directly as it stands because it relies on the read.metharray.sheet() function from minfi which reads a single .csv file and assign a basename to the .idat file depending on the directory provided. Because ChAMP is essentially a wrapper of multiple packages, it is not convenient for such analysis with different directories. You could recreate champ.load() workflow (https://rdrr.io/bioc/ChAMP/src/R/champ.load.R) executing read.metharray.sheet and read.metharray.exp in each of your sub-directory folders and merge the multiple rgSet objects and then it should be fine, but there is a lot of work on the code