ped {pbatR} | R Documentation |
Creates, tests, reads, or writes objects of type ped
or
pedlist
to be used with the pbat commands.
The ped
class inherits the data.frame
structure, and
is almost identical to the data.frame
object described to
create it, only with some special reserved names.
The pedlist
class inherits the list
structure, and is almost
identical to the list
object described to create it, only with
some special reserved names.
The `pped' functions provide support for a more compressed form of input, that can be read in faster, and so may be faster when running in clustered mode.
as.ped( x, pid="pid", id="id", idfath="idfath", idmoth="idmoth", sex="sex", affection="AffectionStatus", clearSym=FALSE ) as.pedlist( x, pid="pid", id="id", idfath="idfath", idmoth="idmoth", sex="sex", affection="AffectionStatus", clearSym=FALSE ) is.ped( obj, pure.ped=FALSE ) is.pedlist( obj ) read.ped( filename, format="ped", lowercase=TRUE, sym=TRUE, max=100, ... ) fread.ped( filename, ... ) write.ped( file, ped ) is.pped( obj ) read.pped( filename, max=100 ) as.pped( ped, ppedname="" ) ## S3 method for class 'ped': sort(x,decreasing=FALSE,...) plotPed( ped, sink=NULL ) ped.markerNames( ped )
x |
An object of class ped , pedlist , data.frame , or list as
described below.
If x is of class ped or pedlist , no other options are used.
When x is of class data.frame , the columns have entries
that match the string parameters idped,...,AffectionStatus ;
genetic markers consist of subsequent columns
formated as follows: e.g. marker `p5' would need
two columns known as `p5.a' `p5.b' (or really
just where the characters a and b are different).
When x is of class list , the
entries still include idped,...,censor as discussed
previously, and genetic markers consist of a list object of two
vectors for each unphased haplotype.
|
pid |
String corresponding to column name for pedigree id. |
id |
String corresponding to column name for subject id. |
idfath |
String corresponding to column name for father id. |
idmoth |
String corresponding to column name for mother id. |
sex |
String corresponding to column name for sex. |
affection |
String corresponding to column name for affection status. |
filename |
Filename to open; does not need .phe extension. |
format |
Toggles the return structure, set to "ped" or "pedlist". |
lowercase |
When TRUE (and sym is FALSE), enforces all headers to lowercase for convenience. |
... |
Options for read.table , used only when sym is
FALSE. 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 |
ped |
an object of class ped or pedlist (see
as.ped or as.pedlist ) |
obj |
an object |
sym |
When TRUE, only the header of the file is read in; only PBAT will load in the file. When FALSE, the entire file will be read in, and can be modified before using with PBAT. |
max |
When sym is TRUE, the amount of headers to read in before going pure symbolic (so that the SNP usage consistency will not be assessed by pbatR, only by PBAT). |
clearSym |
When TRUE, if a symbolic file is found, it will be read in; otherwise, it will stay symbolic. |
pure.ped |
When FALSE, tests if an object is a `ped' or `pped'. When TRUE, tests only if the object is a `ped'. |
ppedname |
Name of the `pped' file. If a symbolic ped, it defaults to that name except with a pped extension; otherwise, it defaults to `pped.pped'. |
decreasing |
Whether to sort in decreasing/increasing order. |
sink |
For `plot.ped', this is the name of a pdf file to output all of the plots to (there will be one plot per page). |
When reading in a file on disk using read.ped
, a `.ped' file should
have the following format (taken from the PBAT web-page).
The first line of the PBAT pedigree file contains the names of the
markers.
Each subsequent line stands for one individual/subject, starting with
the pedigree id, followed by the individual/subject id, the id of the
father, the id of the mother, the individual's sex and affection
status. After this information, for each marker, both marker alleles
are listed. The order of the markers has to correspond to the order of
the marker names in the first line of the file. Missing values here
must be encoded with a `0', unlike the phenotype file.
Examples of this type of file can be found on the PBAT webpage.
The usage of as.ped
and as.pedlist
should also follow
the same missingness convention.
`plot.ped' attempts to make use of the `kinship' package to draw the pedigrees. In my personal experience, this package cannot handle all pedigrees. My preferred alternative would be to use Madeline, which makes beautiful pictures (amongst other things): http://eyegene.ophthy.med.umich.edu/
ped.markerNames
returns the names of the markers, without the '.a' and '.b' extension for markers (and not duplicated for markers).
http://www.biostat.harvard.edu/~clange/default.htm
http://www.people.fas.harvard.edu/~tjhoffm/pbatR.html
read.ped
,
write.ped
,
as.pedlist
# A highly artificial example with not enough subjects to be run; # however, it demonstrates how to put data in it. x <- data.frame( pid = c(1,1,1,1,1), id = c(1,2,3,4,5), idfath = c(4,4,4,0,0), idmoth = c(5,5,5,0,0), sex = c(1,2,1,1,2), AffectionStatus = c(1,0,0,1,0), m1.a = c(1,1,1,1,1), m1.b = c(1,2,1,1,2), m2.a = c(4,4,4,4,4), m2.b = c(3,3,3,4,3) ) x myPed <- as.ped( x ) # Mark it with the class 'ped' myPedlist <- as.pedlist( x ) # Instead mark it with 'pedlist' myPed myPedlist # an alternate example of creating names( x )[1:6] <- c( "mypedid", "subid", "fathid", "mothid", "gender", "affection" ); x myPed <- as.ped( x, pid="mypedid", id="subid", idfath="fathid", idmoth="mothid", sex="gender", affection="affection" ) myPed # Note it's the same as before! myPed <- as.ped( myPedlist ) # Easy conversion back myPedlist <- as.pedlist( myPed ) # and forth between formats.