Description Usage Arguments Value Author(s)
View source: R/features-prediction.R
Identification of splice junctions and exons for a given chromosome and strand.
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)
|
file_bam |
BAM file with genomic RNA-seq read alignments |
paired_end |
Logical, |
which |
|
min_junction_count |
Minimum fragment count required for a splice
junction to be included. If specified, argument |
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 |
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 |
sample_name |
Sample name used in messages |
verbose |
If |
GRanges
of predicted features
Leonard Goldstein
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