getSGFeatureCountsPerSample {SGSeq} | R Documentation

## Compatible fragment counts for splice graph features

### Description

Obtain counts of compatible fragments for splice graph features.

### Usage

    getSGFeatureCountsPerSample(features, file_bam, paired_end, sample_name,
      min_anchor, retain_coverage, verbose, cores)

### Arguments

`features` | `SGFeatures` object
`file_bam` | BAM file with genomic RNA-seq read alignments
`paired_end` | Logical, `TRUE` for paired-end data, `FALSE` for single-end data
`sample_name` | Sample name used in messages
`min_anchor` | Integer specifiying minimum anchor length
`retain_coverage` | Logical indicating whether coverage for each exon should be retained as an `RleList` in metadata column “coverage”. This allows filtering of features using more stringent criteria after the initial prediction.
`verbose` | If `TRUE`, generate messages indicating progress
`cores` | Number of cores available for parallel processing

### Value

Numeric vector of compatible fragment counts

### Author(s)

Leonard Goldstein

[Package SGSeq version 1.16.2 Index]