SGSeq (version 1.4.0)

analyzeVariants: Analysis of splice variants

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, 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. If the denominator is smaller than min_denominator, variant frequencies are set to NA. If NA, all variant frequencies are returned.

cores

Number of cores available for parallel processing

Value

An SGVariantCounts object

Examples

sgvc <- analyzeVariants(sgfc_pred)