pbatR (version 0.7)

phe: Phenotype Object

Description

Creates, tests, reads, or writes an object of class phe.

Usage

as.phe( df, pid="pid", id="id" )
is.phe( obj )
read.phe( filename, na.strings=c("-",".","NA"), lowercase=TRUE, ... )
write.phe( file, phe )

Arguments

df

Dataframe with the data

pid

String for the column header for 'pid' - pedigree ID.

id

String for the column header for 'id' - subject ID.

obj

any object

filename

Filename to open; does not need .phe extension.

na.strings

Strings that represent NA; defaults should be fine here.

lowercase

When TRUE (default), enforces all headers to lowercase for convenience.

...

Options for read.table. Do not put in header=TRUE, as this will cause an error, as the header is automatically loaded.

With the proper file formatting, this should not

file

string representing filename, or a connection for file output

phe

An object of class 'phe' (see as.phe).

Details

When reading in a file on disk using read.ped, a `.phe' file should have the following format (taken from the PBAT web-page). The first line contains the names of the covariates and phenotypes and the subsequent lines contain the pedigree id, the id of the subject, followed by the values of the covariates and phenotypes for that subject. Here missing values must be indicate with a `.' or `-', unlike the pedigree file. Examples of this type of file can be found on the PBAT webpage. Once the dataset is read in, missing values are converted into the usual R format of NA (see NA in the help files).

When using as.phe, missing values should be in the native R format. The write.ped function will convert back into the missing format necessary for PBAT.

References

http://www.biostat.harvard.edu/~clange/default.htm http://www.people.fas.harvard.edu/~tjhoffm/pbatR.html

See Also

read.ped, write.ped, as.ped, as.pedlist

Examples

# A highly artificial example just to get you used to the syntax
#  of using 'as.phe'.
x <- data.frame( pid    = c(1,1,2,2,2),
                 id     = c(1,2,3,4,5),
                 age    = c(14,45,33,22,21),
                 weight = c(150,100,180,185,110) )
x
myPhe <- as.phe( x );
myPhe

# And just another e.g. capitolizing on prior code
names(x)[1:2] <- c("thepid","theid")
x
myPhe <- as.phe( x, pid="thepid", id="theid" )
myPhe  # same as before!