Usage
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