Allele-specific TF activity computed within each donor

Source: R/DsASC-tfactivity.R

Repeats ascTFActivity separately for each donor's samples in a given condition, so a pooled result can be checked for donor robustness (i.e. that it is not driven by one deep donor). Per-donor coverage is lower, so some TFs will drop below minSites in some donors – that is expected and is part of the robustness read-out.

ascTFActivityByDonor(
  refMat,
  altMat,
  deltaDt,
  annot,
  condition,
  stimCol = "stimulus",
  minDonorSamples = 1L,
  ...
)

Arguments

refMat, altMat

count matrices [snp x sample].

deltaDt

motif delta table (snpId, tf, delta); subset to the TFs of interest beforehand to keep this fast.

annot

sample annotation with sampleId, donor and the condition column.

condition

value of stimCol to select (e.g. "U" or "S").

stimCol

name of the condition column (default "stimulus").

minDonorSamples

minimum samples a donor must have in the condition (default 1).

...

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

Value

data.table with per-(TF, donor) activity plus donor, condition; NULL if nothing computable.

Author

Irem B. GUNDUZ