analyzeVariants: Analysis of splice variants

In ldg21/SGSeq: Splice event prediction and quantification from RNA-seq data

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

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

sgvc <- analyzeVariants(sgfc_pred)

ldg21/SGSeq documentation built on Oct. 14, 2020, 9:51 p.m.