R: function to do primitive trait quality control

check.trait {GenABEL} | R Documentation

## function to do primitive trait quality control

### Description

This function check for outliers (using FDR framework) and plots the raw data.

### Usage

    check.trait(trait, data, fdrate = 0.05, graph = TRUE, binshow = FALSE,
    		qoption = "bh95")

### Arguments

`trait` | name (or list of names) of trait(s) to be checked
`data` | gwaa.data object or data frame containing the trait
`fdrate` | false discovery rate to apply for QC
`graph` | if graphical output should be produced
`binshow` | if binary traits should be plotted
`qoption` | how to compute q-values (not implemented, currently using only BH95)

### Details

The P-value that a particulat measurment is an outlier is compted as folowing. Consider trait vector Y with particulat i^{th} measurment denodet as y_i. Let Y(-i) is vector, which is the same as Y, except that i^{th} measurment is dropped. Then Chi-square for measurment i is computed as

Chi_{i} = (mean(Y(-i)) - y_i)^2/var(Y(-i))

P-value is computed using 1 d.f., and the vector of P-values enters FDR computation procedure (BH95 by default).

### Value

No value returned, output is made to the screen and graphical device.

### Author(s)

Yurii Aulchenko

### See Also

`check.marker`

### Examples

    require(GenABEL.data)
    data(srdta)
    check.trait("qt3",data=srdta)
    n <- names(srdta@phdata)
    check.trait(n,data=srdta)

[Package GenABEL version 1.8-0 Index]