daseq: Differential activity analysis (DASeq)

In fchen365/surf: Statistical Utility for RBP (RNA binding protein) Functions

Description

Detect differential activity using the AUC measure and RNA-seq quantification. For more details about methodology, see Details. This function can be used as part of SURF or as well a stand-along analysis. For the former, input a surf object to event. For the latter, input targetSets and optionally controlSets.

Usage

daseq(
  event = NULL,
  rankings,
  sampleData,
  target.type = "transcript",
  targetSets = NULL,
  controlSets = NULL,
  n.sample = 1000,
  cores = max(1, detectCores() - 2),
  verbose = FALSE,
  ...
)

Arguments

event	a surf object from faseqInfer or faseq.
rankings	a SummarizedExperiment object from getRankings.
sampleData	data.frame, external samples, which contain condition column, whose row names must match the column names of rankings.
target.type	character(1), either "transcript" or "gene".
targetSets	a named list of character, the target IDs.
controlSets	a named list of character, the control IDs.
n.sample	integer, number of times of controlSet sampling, default to 1000.
cores	integer, number of computing cores.
verbose	logical, whether (TRUE) to echo progress.
...	additional parameters for AUCell::AUCell_calcAUC.

Value

a daseqResults object if targetSets was given, or a surf object if event was give.

References

Chen, F., & Keles, S. (2020). SURF: integrative analysis of a compendium of RNA-seq and CLIP-seq datasets highlights complex governing of alternative transcriptional regulation by RNA-binding proteins. Genome Biology, 21(1), 1-23.

fchen365/surf documentation built on June 18, 2021, 12:02 p.m.