phe {pbatR}R Documentation

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 be used.
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.

Note

`read.phe' mild warning: This function might change the names of headers, so they may not correspond to what pbat is looking for if you call any of the pbat*files() commands (even if lowercase=FALSE, as some symbols might be modified by R naming conventions).

`read.phe' mild warning solution: For example, instead of using pbat.logrank.files(...), just use the suggested pbat.m(...) or pbat.obj(..) after loading in the `.phe' and `.ped' files.

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!

[Package pbatR version 0.8 Index]