read.single.bed: read.single.bed

In RnBeads: RnBeads

Description

reads a BED file with methylation information

Usage

read.single.bed(
  file,
  chr.col = 1L,
  start.col = 2L,
  end.col = 3L,
  strand.col = 6L,
  mean.meth.col = 7L,
  coverage.col = 8L,
  c.col = NA,
  t.col = NA,
  is.epp.style = FALSE,
  coord.shift = 0L,
  ffread = FALSE,
  context = "cg",
  ...
)

Arguments

file	the input BED file
chr.col	chromosome column index
start.col	start column index
end.col	end column index
strand.col	strand column index
mean.meth.col	mean methylation column index
coverage.col	column with coverage information
c.col	converted C counts column index
t.col	unconverted C counts column index
is.epp.style	Flag for custom Broad Epigenome Pipeline (EPP) bed style (columns "chrom", "start", "end", "methylated_count/total_count", "meth_score_scaled_0_1000" and "strand" in this order). Setting this to TRUE overwrites all other parameters except file, and also neglects ....
coord.shift	An integer specifying the coordinate adjustment applied to the start and end coordinates.
ffread	Use ff package functionality
context	prefix for the output rownames
...	further arguments to read.table or read.table.ffdf

Details

Missing columns should be assigned with NA. In case mean.meth.col is absent at least coverage.col and one of c.col or t.col should be specified.

Value

a data.frame or ff.data.frame object with DNA methylation and coverage information. The row names are formed by the following convension: context\.read.delim(file,...)[,chr.col]\.read.delim(file,...)[,start.col]\.read.delim(file,...)[,strand.col].

Author(s)

Pavlo Lutsik

RnBeads documentation built on March 3, 2021, 2 a.m.