filterWhippetEvents: Filter out significant events from a whippet diff comparison
In GeneStructureTools: Tools for spliced gene structure manipulation and analysis

Description Usage Arguments Value Author(s) See Also Examples

Filter out significant events from a whippet diff comparison

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

`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.

filtered whippet differential comparison data.frame

Beth Signal

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

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