filterTranscriptMetadata: Prepare transcript metadata before extending truncated...

Description Usage Arguments Value

View source: R/processEnsemblAnnotations.R

Description

Retain only genes with >= 2 transcripts and mark CDS start and end 'not found' for incomplete transcripts.

Usage

1
2
3
4
filterTranscriptMetadata(transcript_metadata,
  complete_transcripts = c("protein_coding", "lincRNA"),
  incomplete_transcripts = c("nonsense_mediated_decay",
  "processed_transcript", "retained_intron"))

Arguments

transcript_metadata

Data frame of transcript metadata.

complete_transcripts

Biotypes of complete transcripts (CDS start and end NF flags extracted grom GFF)

incomplete_transcripts

Biotypes of trnascripts whose start and end are likely to be missing.

Value

Filtered transcript metadata df.


kauralasoo/reviseAnnotations documentation built on Oct. 22, 2017, 3:13 p.m.