analyzeVariants {SGSeq} | R Documentation

## 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, 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)

[Package SGSeq version 1.28.0 Index]