MakeBED: Export MWAS results in BED format.

In ramwas: Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms

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

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 [e-mail]

See Also

See vignettes: browseVignettes("ramwas").

Examples

## 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. 8, 2020, 8:24 p.m.