read.single.bed: read.single.bed

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 @param chr.col chromosome column index @param start.col start column index @param end.col end column index @param strand.col strand column index

mean.meth.col

mean methylation column index @param c.col converted C counts column index @param t.col unconverted C counts column index

coverage.col

column with coverage information @param 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 .... @param coord.shift An integer specifying the coordinate adjustment applied to the start and end coordinates. @param ffread Use ff package functionality @param context prefix for the output rownames @param ... 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.

@return 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 Pavlo Lutsik @export