sextest: Test Illumina methylation 450K array probes for sex...
In wateRmelon: Illumina 450 methylation array normalization and metrics

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

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.

1	sextest(betas, sex, ...)

`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`

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

Leonard.Schalkwyk@kcl.ac.uk

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

seabi seabird

   #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)