blat2exons: Take coordinates of blat matches and split into a single line...

In sherrillmix/dnar: Miscellaneous functions to deal with bioinformatic analyses

Take coordinates of blat matches and split into a single line for each exon

Description

Take coordinates of blat matches and split into a single line for each exon

Usage

blat2exons(
  chroms,
  names,
  starts,
  ends,
  strands = rep("+", length(names)),
  lengths = TRUE,
  extraCols = NULL,
  extraSplits = NULL,
  prefix = "ex",
  adjustStart = 0
)

Arguments

chroms	Chromosome or other identifier
names	Name of gene of other container of exons
starts	Start coordinates of exons
ends	End coordinates of exons if lengths is FALSE or length of exon if lengths is TRUE
strands	Strand (for numbering exons in reverse on - strand)
lengths	logical whether ends are end coordinates or lengths
extraCols	a dataframe of extra columns (1 per batch of starts) to be added to the output
extraSplits	a dataframe of extra comma-separated values (1 string of comma separated values per batch of starts, 1 value per start-stop pair) to be added to the output
prefix	prefix to be added to exon names
adjustStart	add adjustStart to starts (good for 0 index start, 1 index ends of UCSC)

Value

data.frame with a row for each exon or piece of alignment and columns chrom, name, exonName, start, end and strand

Examples

blat2exons(
  c('chr1','chr1','chr2'),
  c('read1','read2','read1'),
  c('1,100','50,150,300','1000,2000,3000'),
  c('20,200','50,50,100','999,999,1234'),
  c('+','-','+')
)

sherrillmix/dnar documentation built on July 18, 2022, 10:07 p.m.