processLNCipedia: Process LNCipedia bed-file

In frankRuehle/systemsbio: Streamlined Analysis and Integration of Systems Biology Data

Description

Load and/or modify lncRNA data from LNCipedia.

Usage

processLNCipedia(
  LNCipedia,
  collapseTranscripts2Genes = T,
  makeExonRanges = T,
  addBases = c(0, 0)
)

Arguments

LNCipedia	Either character with filepath to LNCipedia bed-file (no header), dataframe or GRanges object made from LNcipedia bed-file.
collapseTranscripts2Genes	logical. If TRUE, all transcripts of a gene are assigned with the coordinates of the corresponding gene. Recommended for plotting to reduce complexity.
makeExonRanges	logical. If True, an GRanges object for exons is generated using the "blockStarts" and "blockSizes" data from LNCipedia. Transcript or gene coordinates are stored in metadata.
addBases	numeric. Vector with 2 values to be added to each start end position of the ranges. E.g. enter addBases= c(1,0) for transforming 0-based 1-based start coordinate or addBases= c(-10,10) to extend each range for 10 bases to both sides. Omitted if NULL.

Details

LNCipedia date is loaded from bed file or provided as dataframe or GRanges object. For reducing complexity in plotting purposes, all transcripts belonging to a lncRNA gene are given with respective gene coordinates. For each transcript, exon ccordinates are calculated from "blockStarts" and "blockSizes" data from LNCipedia.

Value

GRanges object containing LNCipedia transcripts or exons

Author(s)

Frank Ruehle

frankRuehle/systemsbio documentation built on Sept. 14, 2020, 1:18 a.m.