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Last data update: 2014.03.03

R: function to do primitive trait quality control

check.trait

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

Examples

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

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(GenABEL)
Loading required package: MASS
Loading required package: GenABEL.data
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/GenABEL/check.trait.Rd_%03d_medium.png", width=480, height=480)
> ### Name: check.trait
> ### Title: function to do primitive trait quality control
> ### Aliases: check.trait
> ### Keywords: misc
> 
> ### ** Examples
> 
> require(GenABEL.data)
> data(srdta)
> check.trait("qt3",data=srdta)
--------------------------------
Trait qt3 has 2489 measurements
Missing: 11 ( 0.44 %)
Mean = 2.60859 ; s.d. = 1.101154 
NO outliers discovered for trait qt3 
> n <- names(srdta@phdata)
> check.trait(n,data=srdta)
--------------------------------
trait id is not numeric, skipping
--------------------------------
Trait sex has 2500 measurements
Missing: 0 ( 0 %)
Mean = 0.51 ; s.d. = 0.5 
NO outliers discovered for trait sex 
--------------------------------
Trait age has 2500 measurements
Missing: 0 ( 0 %)
Mean = 50.0378 ; s.d. = 7.060125 
NO outliers discovered for trait age 
--------------------------------
Trait qt1 has 2497 measurements
Missing: 3 ( 0.12 %)
Mean = -0.2981097 ; s.d. = 1.000527 
Outliers discovered for trait qt1 :
p691
-4.6
--------------------------------
Trait qt2 has 2500 measurements
Missing: 0 ( 0 %)
Mean = 6.122224 ; s.d. = 30.60056 
Outliers discovered for trait qt2 :
p4 p14 p26
888 888 888
--------------------------------
Trait qt3 has 2489 measurements
Missing: 11 ( 0.44 %)
Mean = 2.60859 ; s.d. = 1.101154 
NO outliers discovered for trait qt3 
--------------------------------
Trait bt has 2489 measurements
Missing: 11 ( 0.44 %)
Mean = 0.4997991 ; s.d. = 0.5001004 
NO outliers discovered for trait bt 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>