MakeBED: Export MWAS results in BED format.

Description Usage Arguments Details Value Author(s) See Also Examples

Description

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.

Usage

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madeBED(x, filename)
madeBEDrange(x, filename, chr, start, end)
madeBEDgraph(x, filename)
madeBEDgraphRange(x, filename, chr, start, end)

Arguments

x

Name of MWAS directory (parameter dirmwas) or list of RaMWAS parameters as described in the "RW6_param.Rmd" vignette.
Try: vignette("RW6_param","ramwas").

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.

Details

The function returns the MWAS results with locations.

Value

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

Author(s)

Andrey A Shabalin [email protected]

See Also

See vignettes: browseVignettes("ramwas").

Examples

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## 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)

ramwas documentation built on Nov. 29, 2019, 2 a.m.