predictTxFeaturesPerStrand: Identification of splice junctions and exons for a given...
In ldg21/SGSeq: Splice event prediction and quantification from RNA-seq data

Description Usage Arguments Value Author(s)

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

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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)

`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