predictTxFeaturesPerStrand {SGSeq} | R Documentation

## Identification of splice junctions and exons for a given chromosome and strand

### Description

Identification of splice junctions and exons for a given chromosome and strand.

### Usage

    predictTxFeaturesPerStrand(file_bam, paired_end, which, min_junction_count, psi,
      beta, gamma, min_anchor, include_counts, retain_coverage, junctions_only,
      max_complexity, sample_name, verbose)

### Arguments

`file_bam` | BAM file with genomic RNA-seq read alignments
`paired_end` | Logical, `TRUE` for paired-end data, `FALSE` for single-end data
`which` | `GRanges` of genomic regions to be considered for feature prediction, passed to `ScanBamParam`
`min_junction_count` | Minimum fragment count required for a splice junction to be included. If specified, argument `alpha` is ignored.
`psi` | Minimum splice frequency required for a splice junction to be included
`beta` | Minimum relative coverage required for an internal exon to be included
`gamma` | Minimum relative coverage required for a terminal exon to be included
`min_anchor` | Integer specifiying minimum anchor length
`include_counts` | Logical indicating whether counts of compatible fragments should be included in metadata column “N”
`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.
`junctions_only` | Logical indicating whether predictions should be limited to identification of splice junctions only
`max_complexity` | Maximum allowed complexity. If a locus exceeds this threshold, it is skipped, resulting in a warning. Complexity is defined as the maximum number of unique predicted splice junctions overlapping a given position. High complexity regions are often due to spurious read alignments and can slow down processing. To disable this filter, set to `NA`.
`sample_name` | Sample name used in messages
`verbose` | If `TRUE`, generate messages indicating progress

### Value

`GRanges` of predicted features

### Author(s)

Leonard Goldstein

[Package SGSeq version 1.24.0 Index]