filterRmatsEvents: Filter out significant events from a RMATS dataset

In betsig/GeneStructureTools: Tools for spliced gene structure manipulation and analysis

Description

Filter out significant events from a RMATS dataset

Usage

filterRmatsEvents(
  rmatsDataSet,
  FDR = 0.05,
  psiDelta = 0.1,
  idList = NA,
  minCounts = NA,
  medianCounts = NA,
  sampleTable
)

Arguments

rmatsDataSet	rmatsDataSet generated from readRmatsDataSet()
FDR	maximum FDR required to call event as significant
psiDelta	minimum change in psi required to call an event as significant
idList	(optional) list of gene ids to filter for
minCounts	minumum number of counts for all replicates in at least one condition to call an event as significant
medianCounts	median count for all replicates in at least one condition to call an event as significant
sampleTable	data.frame with sample names and conditions. Only needed if filtering with counts.

Value

filtered rmatsDataSet

Author(s)

Beth Signal

See Also

Other rmats data processing: altIntronRmats(), altSpliceSiteRmats(), annotateEventCoords(), annotateOverlapRmats(), betweenNumbers(), duplicateReference(), exonsToIntrons(), extractEvent(), readRmatsDataSet(), reformatExons(), removeDuplicatePairs(), removeExonsBetween(), rmatsTranscriptChangeSummary(), skipExonByJunction(), splitLongExons()

Examples

rmats_directory <- system.file("extdata", "rmats_small/", package = "GeneStructureTools")
rds <- readRmatsDataSet(rmats_directory)
rds.filtered <- filterRmatsEvents(rds, FDR = 0.01, psiDelta = 0.1)
# filter by gene name/id
rds.Tmem208 <- filterRmatsEvents(rds, idList = "Tmem208", FDR = 1, psiDelta = 0)

betsig/GeneStructureTools documentation built on March 31, 2021, 4:43 a.m.