Subset of the packed .cx file

Subset samples

yame subset will subset the samples from the multi sample .cx file. We can store the samples we want to keep with a text file or simply providing them in the command line. Make sure the sample names provided is in the sample names of .cx file.

yame subset -l sample.txt yourfile.cg

To extract one term of format 2 to format 0, you can use the yame subset -s function.

For more help with subset, run yame subset in the terminal or check out the subset help page.

Subset cx sites

If we want to obtain methylation sites from specific regions, we can use this yame rowsub function. If we have a list of CpG sites we want to subset, for example

chr16_18300002
chr16_18300046
chr16_18300140
chr16_18300162
chr16_18300172

We can use -L with -R together (we provided two row coordiante .cr files mm10/hg38).

yame rowsub -R cpg_nocontig.cr -L CpG_sites.tsv yourfile.cg > subset.cg

For more help with rowsub, run yame rowsub in the terminal or check out the rowsub help page.