Subsetting specific comparisons

[Majd Abdulghani]

Hello!

I have 6 comparisons in my SwitchList, which means I can't create an overlap Venn diagram with extractSwitchOverlap() because it takes a maximum of 5 comparisons. Is there a way to subset 2-3 comparisons from my SwitchList? I couldn't figure out how to make it work with subsetSwitchAnalyzeRlist().

Thank you!

Majd

[Kristoffer Vitting-Seerup]

You would need to use subsetSwitchAnalyzeRlist() on both condition_1 and condition_2 in isoformFeatures entry of the of the switchAnalyzeRlist.

[Majd Abdulghani]

Gotcha. I did this and it worked:

subsettedList <- subsetSwitchAnalyzeRlist(
  switchAnalyzeRlist = SwitchList,
  subset = (ssSwitchList[["isoformFeatures"]]$condition_1 %in% c("NTC_noIR", "KD_noIR") &
              ssSwitchList[["isoformFeatures"]]$condition_2 %in% c("NTC_IR", "KD_noIR", "KD_IR"))
)