wm-port: Functions imported from wateRmelon

In bigmelon: Illumina methylation array analysis for large experiments

Description

Manual page for methods for the extraenous functions from wateRmelon. For more details for specific functions see the respective manual pages in wateRmelon.

Usage

## S4 method for signature 'gdsn.class,gdsn.class'
qual(norm, raw)
## S4 method for signature 'gds.class'
predictSex(x, x.probes=NULL, pc=2, plot=TRUE, irlba=TRUE, center=FALSE, scale.=FALSE)
## S4 method for signature 'gdsn.class'
predictSex(x, x.probes=NULL, pc=2, plot=TRUE, irlba=TRUE, center=FALSE, scale.=FALSE)

Arguments

norm	normalized node (gdsn.class)
raw	raw node (gdsn.class)
x	gdsclass object or node corresponding to betas
x.probes	Default is NULL, is required to be supplied in bigmelon. logical or numeric vector containing indicies of X chromosome probes
pc	The principal component to guess sex across (usually the 2nd one in most cases)
plot	Logical, indicated whether or not to plot the prediction
irlba	Logical, indicate whether or not to use the faster method to generate principal components
center	Logical, indicate whether or not to center data around 0
scale.	Logical, indicate whether or not to scale data prior to prcomp

Details

For the full usage and description of any functions that link to this manual page, please visit the respective manual pages from wateRmelon.

Value

Returns expected output of functions from wateRmelon

See Also

wateRmelon

bigmelon documentation built on Nov. 8, 2020, 7:40 p.m.