refine_transcripts_by_annotation: Refine called transcripts by an existing transcript model

In Maxim-Ivanov/TranscriptomeReconstructoR: Data-driven Annotation of the Transcriptome

Refine called transcripts by an existing transcript model

Description

Refine called transcripts by an existing transcript model

Usage

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:

• 5'- and 3'-borders of called exons are adjusted to the most similar border of an annotated exon (by not more than max_exon_diff bp);

• Annotated transcripts are classified into valid and non-valid. A valid known transcript must overlap with called TSS and PAS (both having scores above min_score_2) within tx_flanks_up and tx_flanks_down bp windows around its start and end, respectively;

• 5'- and/or 3'-borders of called MC and LC transcripts lacking overlap with TSS and/or PAS are adjusted to the borders of the most similar mate among the valid annotated transcripts (given that at least min_tx_cov fraction of the called transcript is covered by the annotated mate);

• Valid annotated transcripts which do not overlap with any called transcript are copied from the annotation to the called HC transcript set;

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 Oct. 3, 2023, 11:19 p.m.