Allele-specific TF activity across conditions, with a switch (handoff) score

Source: R/DsASC-tfactivity.R

Runs ascTFActivity separately in two contexts (e.g. resting vs stimulated) and joins them, adding the change in activity deltaObs = obs_B - obs_A and a flip flag for TFs whose activity changes sign between contexts. These are candidate "dynamic TF handoffs".

ascTFActivitySwitch(
  refMat,
  altMat,
  deltaDt,
  samplesA,
  samplesB,
  labelA = "A",
  labelB = "B",
  ...
)

Arguments

refMat, altMat

count matrices [snp x sample].

deltaDt

motif delta table (snpId, tf, delta).

samplesA, samplesB

sample vectors for the two contexts.

labelA, labelB

context labels (default "A"/"B").

...

passed to ascTFActivity (prefDelta, minReads, ...).

Value

data.table with per-TF activity in both contexts plus deltaObs, flip.

Author

Irem B. GUNDUZ