geneLevelStats: geneLevelStats

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

geneLevelStats

Description

Aggregates bin-level statistics to the gene-level

Usage

geneLevelStats(
  se,
  coef = NULL,
  excludeTypes = NULL,
  includeTypes = NULL,
  returnSE = TRUE,
  minDensityRatio = 0.1,
  minWidth = 20,
  excludeGeneAmbiguous = TRUE
)

Arguments

se	A 'RangedSummarizedExperiment' containing the results of one of the DEU wrappers.
coef	The coefficients tested (if the model included more than one term).
excludeTypes	Vector of bin types to exclude.
includeTypes	Vector of bin types to include (overrides 'excludeTypes')
returnSE	Logical; whether to return the updated 'se' object (default), or the gene-level table.
minDensityRatio	Minimum ratio of read density (with respect to the gene's average) for a bin to be included.
minWidth	Minimum bin width to include
excludeGeneAmbiguous	Logical; whether to exclude bins which are ambiguous (i.e. can be from different genes)

Value

If 'returnSE=TRUE' (default), returns the 'se' object with an updated 'metadata(se)$geneLevel' slot, otherwise returns the gene-level data.frame.

Examples

library(SummarizedExperiment)
data(example_bin_se)
se <- diffSpliceWrapper(example_bin_se, ~condition)
se <- geneLevelStats(se, includeTypes="3UTR")
head(metadata(se)$geneLevel)

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