phe {pbatR} | R Documentation |
Creates, tests, reads, or writes an object of class phe
.
as.phe( df, pid="pid", id="id" ) is.phe( obj ) read.phe( filename, na.strings=c("-",".","NA"), lowercase=TRUE, ... ) write.phe( file, phe )
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 ). |
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.
`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.
http://www.biostat.harvard.edu/~clange/default.htm
http://www.people.fas.harvard.edu/~tjhoffm/pbatR.html
read.ped
,
write.ped
,
as.ped
,
as.pedlist
# 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!