DEUwrappers: DEUwrappers

In ETHZ-INS/diffUTR: diffUTR: Streamlining differential exon and 3' UTR usage

DEUwrappers

Description

Wrappers around commonly-used DEU methods (diffSpliceDGE, DEXSeq and an improved version of diffSplice

Usage

diffSpliceDGEWrapper(
  se,
  design,
  coef = NULL,
  QLF = TRUE,
  robust = TRUE,
  countFilter = TRUE,
  excludeTypes = NULL
)

diffSpliceWrapper(
  se,
  design,
  coef = NULL,
  robust = TRUE,
  improved = TRUE,
  countFilter = TRUE,
  excludeTypes = NULL
)

DEXSeqWrapper(
  se,
  design = ~sample + exon + condition:exon,
  reducedModel = ~sample + exon,
  excludeTypes = NULL,
  ...
)

Arguments

se	A bin-wise SummarizedExperiment as produced by countFeatures
design	A formula (using columns of 'colData(se)') or (for 'diffSpliceWrapper' or 'diffSpliceDGEWrapper' only) a model.matrix.
coef	The coefficient to be tested (ignored for 'DEXSeqWrapper').
QLF	Logical; whether to use edgeR's quasi-likelihood negative binomial (applicable only to 'diffSpliceDGEWrapper').
robust	Logical; whether to use robust fitting for the dispersion trend (ignored for 'DEXSeqWrapper').
countFilter	Logical; whether to filter out low-count bins (ignored for 'DEXSeqWrapper').
excludeTypes	A vector of bin types to ignore for testing. To test for any kind of differential usage, leave empty. To test for differential UTR usage, use 'excludeTypes=c("CDS","non-coding")' (or see geneLevelStats for more options).
improved	Logical; whether to use diffSplice2 instead of the original diffSplice (default TRUE).
reducedModel	A reduced formula (applicable only to 'DEXSeqWrapper').
...	Further arguments (passed to 'testForDEU' and 'estimateExonFoldChanges') of 'DEXSeq'. Can for instance be used to enable multithreading, by passing 'BPPARAM=BiocParallel::MulticoreParam(ncores)'.

Value

The 'se' object with additional rowData columns contain bin (i.e. exon) -level statistics, and a metadata slot containing gene level p-values.

Examples

library(SummarizedExperiment)
data(example_bin_se)
se <- diffSpliceWrapper(example_bin_se, ~condition)
head(rowData(se))

ETHZ-INS/diffUTR documentation built on Nov. 3, 2024, 6:26 p.m.