sextest: Test Illumina methylation 450K array probes for sex...

In schalkwyk/wateRmelon: Illumina 450 and EPIC methylation array normalization and metrics

Test Illumina methylation 450K array probes for sex difference (internal function for calculating seabi performance metric)

Description

This is a wrapper for lm which does the equivalent of a Student t-test for difference in betas between males and females for each row of a matrix of betas.

Usage

sextest(betas, sex, ...)

Arguments

betas	a matrix of betas, each row is a probe, each column a sample
sex	a factor with 2 levels for male and female
...	additional arguments to be passed to lm

Value

Returns a vector of p-values of length equal to the number of rows of betas

Author(s)

[e-mail]

References

Pidsley R, Wong CCY, Volta M, Lunnon K, Mill J, Schalkwyk LC: A data-driven approach to preprocessing Illumina 450K methylation array data (submitted)

See Also

seabi seabird

Examples

   #MethyLumiSet method
     data(melon)
     sex  <- pData(melon)$sex
     melon.sextest<-sextest(betas(melon),sex)


   #MethyLumiSet method with quality control step
     data(melon)
     melon.dasen <- dasen(melon)
     sex  <- pData(melon.dasen)$sex
     melon.sextest<-sextest(betas(melon.dasen),sex)

schalkwyk/wateRmelon documentation built on April 15, 2024, 12:06 p.m.