filterWhippetEvents {GeneStructureTools}R Documentation

Filter out significant events from a whippet diff comparison

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/",
package = "GeneStructureTools")
wds <- readWhippetDataSet(whippetFiles)
wds <- filterWhippetEvents(wds)
[Package GeneStructureTools version 1.6.0 Index]