diffAUC: Differential activity (via AUC)

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

Description

Detect differential activity using the AUC measure and RNA-seq quantification. This unit is a helper of daseq.

Usage

diffAUC(
  targetSet,
  controlSet = NULL,
  rankings,
  sampleData,
  n.sample = 1000,
  cores = 1,
  verbose = FALSE,
  ...
)

Arguments

targetSet	character vector, set of targeted units.
controlSet	character vector, control set for contrast. If NULL (default), the full set of elements in rankings will be used.
rankings	a SummarizedExperiment object, with row corresponding to transcript or gene and column corresponding to samples. Each element is a expression measure (e.g., TPM).
sampleData	data.frame of sample data, which contains a condition column.
n.sample	integer, number of times of controlSet sampling, default to 1000.
cores	integer, number of computing cores.
verbose	logical, whether to print out progress report.
...	additional parameters for AUCell::AUCell_calcAUC.

Value

a data.frame of DASeq results.

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