analyzeVariants: Analysis of splice variants

Description Usage Arguments Value Author(s) Examples

View source: R/main.R

Description

High-level function for the analysis of splice variants from splice graph features. Splice variants are identified with findSGVariants. Representative counts are obtained and variant frequencies estimated with getSGVariantCounts.

Usage

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analyzeVariants(object, maxnvariant = 20, include = "default",
  min_denominator = NA, min_anchor = 1, cores = 1)

Arguments

object

SGFeatureCounts object

maxnvariant

If more than maxnvariant variants are identified in an event, the event is skipped, resulting in a warning. Set to NA to include all events.

include

Character string indicating whether identified splice variants should be filtered. Possible options are “default” (only include variants for events with all variants closed), “closed” (only include closed variants) and “all” (include all variants).

min_denominator

Integer specifying minimum denominator when calculating variant frequencies. The total number of boundary-spanning reads must be equal to or greater than min_denominator for at least one event boundary. Otherwise estimates are set to NA. If NA, all estimates are returned.

min_anchor

Integer specifiying minimum anchor length

cores

Number of cores available for parallel processing

Value

SGVariantCounts object

Author(s)

Leonard Goldstein

Examples

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ldg21/SGSeq documentation built on May 7, 2019, 9:37 a.m.