Closed jdm204 closed 3 years ago
Hey, sorry for the late reply, as just back from the vacation. Yes, I think it could realize your ask after modification, so there are two folder paths, i.e., one is for the case group and another one is for the control groups, then for the replicates within each folder, it would read your files by recognizing the file names, like "case_apple, case_banana...". Is that what you like?
No worries, hope you had a nice vacation!
That would be an improvement, though what I meant was the ability to specify arbitrary file names, something like:
cases <- c("/path/to/case1.gz", "/other/path/case2.gz")
controls <- c("../control1.gz", "/other/path/control2.gz")
Quick_GeneDMRs(case_paths = cases, control_paths = controls)
I think this would help to integrate this package into processing pipelines built in Snakemake, Nextflow etc.
Sounds nice. It looks promisingly useful. I have tried to work it out and then it is working. Thanks a lot for the advices.
Hi, thanks for your work on this package!
Would it be possible to have a function to read in methylation files with custom names? For example a vector of case paths and a vector of control paths to avoid having to rename samples to the "1_1, 1_2..." scheme.