sextest {wateRmelon} | R Documentation

## 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)

Leonard.Schalkwyk@kcl.ac.uk

### 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)

[Package wateRmelon version 1.28.0 Index]