get: Functions for Access to Data, MWAS Results, and Location...

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

Description

Functions for access to data, MWAS results, and location information.

Function getLocations obtains the location information for all variables (CpGs).

Function getMWASandLocations obtains both MWAS results and location information in a single data frame.

Functions getDataByLocation and getMWASrange return the data (coverage) and MWAS results for the selected set of variables (CpGs).

Usage

getLocations(x)
getMWAS(x)
getMWASandLocations(x)
getMWASrange(x, chr, start, end)
getDataByLocation(x, chr, start, end)

Arguments

x	Name of directory or list of RaMWAS parameters as described in the "RW6_param.Rmd" vignette. Try: vignette("RW6_param","ramwas"). If a directory name is provided, it must point to Data (coverage) directory (parameter dircoveragenorm) for getDataByLocation and getLocations MWAS directory (parameter dirmwas) for getMWAS, getMWASandLocations, and getMWASrange
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 functions return the MWAS results and/or locations.

Value

Function getLocations returns a data frame with

chr	Chromosome
start	Start position
end	End position

Function getMWAS returns a data frame with

cor	coverage - phenotype correlation
t.test	t-statistic
p.value	p-value
q.value	q-value (FDR)

If the outcome variable was categorical, columns cor and t.test are replaced with R.squared and F-test.

Functions getMWASandLocations and getMWASrange return a data frame with elements of output of both getLocations and getMWAS

Function getDataByLocation returns a list with

locations	Chromosomal location information for located variables
matrix	Data (coverage) matrix for the selected locations

Author(s)

Andrey A Shabalin [e-mail]

See Also

See vignettes: browseVignettes("ramwas").

Examples

## Not run: 
# Extract locations using parameter vector
getLocations(param)

# Extract locations using directory name
getLocations("/data/myMWAS")


# Extract MWAS using parameter vector
getMWAS(param)

# Extract MWAS using directory name
getMWAS("/data/myMWAS")


# Extract MWAS using parameter vector
getMWASandLocations(param)

# Extract MWAS using directory name
getMWASandLocations("/data/myMWAS")


# Extract MWAS for a region
getMWASrange(param, 1, 123321, 223321)

# Chromosome can be character
getMWASrange(param, "chr1", 123321, 223321)


# Extract data for a region
getDataByLocation(param, 1, 123321, 223321)

# Chromosome can be character
getDataByLocation(param, "chr1", 123321, 223321)

## End(Not run)

ramwas documentation built on Nov. 8, 2020, 8:24 p.m.