Ranges-based identification of splice junctions and exons

Description

Ranges-based identification of splice junctions and exons.

Usage

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predictSpliced(frag_exonic, frag_intron, min_junction_count, psi, beta, gamma,
  min_anchor, include_counts, retain_coverage, junctions_only, max_complexity,
  sample_name, seqlevel, strand)

Arguments

frag_exonic

IRangesList with exonic regions from alignments

frag_intron

IRangesList with introns implied by spliced alignments

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

seqlevel

seqlevel to be processed

strand

strand to be processed

Value

IRanges with predicted features

Author(s)

Leonard Goldstein

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