madeBED {ramwas} | R Documentation |
Functions for exporting MWAS results in BED format files.
Function madeBED
saves MWAS findings in BED format for
all variables (CpGs), while madeBEDrange
selects only variables on
a given chromosome between given locations.
Functions madeBEDgraph
and madeBEDgraphRange
do the same,
but create a file in BedGraph format.
madeBED(x, filename) madeBEDrange(x, filename, chr, start, end) madeBEDgraph(x, filename) madeBEDgraphRange(x, filename, chr, start, end)
x |
Name of MWAS directory (parameter |
filename |
Name of the BED file to create. If file exists, it's overwritten. |
chr |
Chromosome name or number. |
start |
Start position of the genomic region of interest. |
end |
End position of the genomic region of interest. |
The function returns the MWAS results with locations.
Returns a data.frame with BED file content:
chrom |
Chromosome |
chromStart |
Start position |
chromEnd |
End position |
name |
Empty name column. BED format only |
score |
p-value |
Andrey A Shabalin andrey.shabalin@gmail.com
See vignettes: browseVignettes("ramwas")
.
## Not run: # Extract BED file using parameter vector madeBED(param, "file.bed") madeBEDrange(param, "file.bed", 1, 123321, 223321) # Extract BED file using directory name madeBED("/data/myMWAS", "file.bed") madeBEDrange("/data/myMWAS", "file.bed", 1, 123321, 223321) ## End(Not run)