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

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

[Package

*GenABEL* version 1.6-7

Index]