refine_transcripts_by_annotation: Refine called transcripts by an existing transcript model

Description Usage Arguments Value Details

View source: R/Refine_by_annotation.R

Description

Refine called transcripts by an existing transcript model

Usage

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refine_transcripts_by_annotation(
  hml_tx,
  annot_exons,
  tss,
  pas,
  fusion_tx = GenomicRanges::GRangesList(),
  max_exon_diff = 10,
  tx_flanks_up = c(-100, 100),
  tx_flanks_down = c(-100, 100),
  min_score_2 = 5,
  min_tx_cov = 0.95,
  clust_threshold = 0.8,
  min_overlap_fusion = 0.5
)

Arguments

hml_tx, annot_exons, fusion_tx

GRangesList objects.

tss, pas

GRanges objects.

max_exon_diff

Positive integer.

tx_flanks_up, tx_flanks_down

Integer vectors of length 2.

min_score_2

Non-negative numeric.

min_tx_cov

Numeric in the range (0, 1].

clust_threshold

Numeric in the range (0, 1].

min_overlap_fusion

Numeric in the range (0, 1].

Value

List of length 4:

  1. GRanges object (updated HC, MC and LC genes);

  2. GRangesList object (refined HC, MC and LC transcripts);

  3. GRanges object (updated fusion genes);

  4. GRangesList object (updated fusion transcripts);

Details

hml_tx is the called transcript model (the second element in the list returned by the call_transcripts_and_genes() function). fusion_tx is the called set of fusion transcripts (the fourth element in the list returned by the call_transcripts_and_genes() function). annot_exons is a known transcript model (returned by e.g. exonsBy(txdb, by = "tx"), where txdb is a GenomicFeatures object).
The function aims to adjust the called transcripts by the annotated transcripts:

In addition, the set of fusion transcripts is updated by finding called transcripts which overlap at least two valid annotated transcripts (or an annotated and a called transcript) by at least min_overlap_fusion fraction of their lengths.


Maxim-Ivanov/TranscriptomeReconstructoR documentation built on Jan. 28, 2021, 11:47 a.m.