read.single.bed: read.single.bed

Description Usage Arguments Details Value Author(s)

View source: R/dataImport.R

Description

reads a BED file with methylation information

Usage

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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.