filterWhippetEvents: Filter out significant events from a whippet diff comparison

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

Description

Filter out significant events from a whippet diff comparison

Usage

filterWhippetEvents(
  whippetDataSet,
  probability = 0.95,
  psiDelta = 0.1,
  eventTypes = "all",
  idList = NA,
  minCounts = NA,
  medianCounts = NA,
  sampleTable
)

Arguments

whippetDataSet	whippetDataSet generated from readWhippetDataSet()
probability	minimum probability required to call event as significant
psiDelta	minimum change in psi required to call an event as significant
eventTypes	which event type to filter for? default = "all"
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 whippet differential comparison data.frame

Author(s)

Beth Signal

See Also

Other whippet data processing: coordinates(), diffSplicingResults(), formatWhippetEvents(), junctions(), readCounts(), readWhippetDIFFfiles(), readWhippetDataSet(), readWhippetJNCfiles(), readWhippetPSIfiles(), whippetTranscriptChangeSummary()

Examples

whippetFiles <- system.file("extdata", "whippet_small/",
    package = "GeneStructureTools"
)
wds <- readWhippetDataSet(whippetFiles)
wds.signif <- filterWhippetEvents(wds)

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