predictTxFeaturesPerStrand: Identification of splice junctions and exons for a given...

Description Usage Arguments Value Author(s)

View source: R/features-prediction.R

Description

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

Usage

1
2
3
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


ldg21/SGSeq documentation built on May 7, 2019, 9:37 a.m.