read.single.bed {RnBeads} | R Documentation |
reads a BED file with methylation information
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", ...)
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 |
coord.shift |
An integer specifying the coordinate adjustment applied to the start and end coordinates. |
ffread |
Use |
context |
prefix for the output rownames |
... |
further arguments to |
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.
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]
.
Pavlo Lutsik