getIsoPartsList: Parse isoform parts list from annotation

Description Usage Arguments Value

View source: R/prepare.R

Description

Parse the isoform parts list from annotation.

Usage

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getIsoPartsList(
  anno,
  gene_id = getMultiTxGene(anno),
  depth.intron = 300,
  cores = max(1, detectCores() - 2)
)

Arguments

anno

a GRanges object of genome annotation, return by import.

gene_id

character, gene_id"s to analyze, default to all multi-transcript genes.

depth.intron

integer, extended depth into gene's flanks, default to 300 nt.

cores

integer, number of computing cores to use.

Value

a list named by gene_id, each of which contains:

segment

GRanges, genomic data of parts list.

label

integer vector, gene model (0 for intron) and exon numbers (coded as integer 1,2,...).

layout

lgCMatrix, transcript structure.


fchen365/surf documentation built on June 18, 2021, 12:02 p.m.