Description Usage Arguments Details Value Author(s)
reads a BED file with methylation information
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 |
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
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