phe: Phenotype Object

In pbatR: Pedigree/Family-Based Genetic Association Tests Analysis and Power

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, sym=TRUE, ...)
fread.phe(filename, ...)

write.phe(file, phe)

## S3 method for class 'phe'
sort(x,decreasing=FALSE,...)

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.
sym	When TRUE, only the header of the file is read in; only PBAT will load in the file (* - see exception). When FALSE, the entire file will be read in, and can be modified before using with PBAT.
...	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).
x	An object of class 'phe' (see as.phe).
decreasing	Whether to sort in decreasing/increasing order.

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.

(*) Exception. If symbolic is true, the dataset will be temporarily read in under one special circumstance. This is when a stratification variable is used in pbat.m, pbat.obj, or pbat.files. This is because the grouping values must be read in. Alternatively, you can specify these values when calling those functions (see the groups.* options) in 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). In general this should not happen.

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

pbatR documentation built on May 29, 2024, 10:27 a.m.