add.phdata: Adds phenotypic variables to gwaa.data object

In GenABEL: genome-wide SNP association analysis

Description

Adds phenotypic variables to phdata part of an gwaa.data-class object

Usage

  add.phdata(data, newphdata, name)

Arguments

data	an object of gwaa.data-class
newphdata	data frame or a vector with new phenotypic data
name	if 'newphdata' is a vector, the name of new variable should be specified in 'name'

Details

If "newphdata" is a data frame, it is simply merged to the phdata part of the "data", and is sorted according to the right order. In this case, The "newphdata" frame should contain single variable named "id", preferably of "character" class. It may contain "sex" variable, but that will be re-named to avoid duplication with the default sex variable presented in phdata.

If 'newphdata' is a vector, it should be of the same length as the number of people in the 'data' and is assumed to have the same order. In this case, you also need to supply the name of the new phenotype via the 'name' argument

Value

An (updated) object of gwaa.data-class

Author(s)

Yurii Aulchenko

See Also

merge.gwaa.data merge.snp.data

Examples

require(GenABEL.data)
data(srdta)
# take a small subset for this example
srdta <- srdta[1:10,1:5]
srdta
# add single var
rnd <- rnorm(nids(srdta))
srdta1 <- add.phdata(srdta,rnd,name="random")
srdta1
# add > 1 var
# generate id names
ids <- paste("p",c(2,1,7,3,5,9,11,22,27),sep="")
# generate some random trait values
newtra1 <- rnorm(9)
newtra2 <- rnorm(9)
# make data frame
x <- data.frame(id=ids,newtra1=newtra1,newtra2=newtra2)
x
# now add this new trait to the data
srdta1 <- add.phdata(srdta,x)
srdta1

GenABEL documentation built on May 30, 2017, 3:36 a.m.