ped                  package:pbatR                  R Documentation

_P_e_d_i_g_r_e_e _O_b_j_e_c_t

_D_e_s_c_r_i_p_t_i_o_n:

     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.

_U_s_a_g_e:

     as.ped( x,
             pid="pid", id="id", idfath="idfath",
             idmoth="idmoth", sex="sex", affection="affection",
             clearSym=FALSE )

     as.pedlist( x,
                 pid="pid", id="id", idfath="idfath",
                 idmoth="idmoth", sex="sex", affection="affection",
                 clearSym=FALSE )

     is.ped( obj, pure.ped=FALSE )

     is.pedlist( obj )

     read.ped( filename, format="ped", lowercase=TRUE, sym=TRUE, max=100, ... )

     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 )

_A_r_g_u_m_e_n_t_s:

       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,...,censor'; 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).

_D_e_t_a_i_l_s:

     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/

_R_e_f_e_r_e_n_c_e_s:

     <URL: http://www.biostat.harvard.edu/~clange/default.htm>

     <URL: http://www.people.fas.harvard.edu/~tjhoffm/pbatR.html>

_S_e_e _A_l_s_o:

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

_E_x_a_m_p_l_e_s:

     # 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),
                      affection = 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 need not be
                                                      #  specified here
     myPed  # Note it's the same as before!

     myPed <- as.ped( myPedlist )       # Easy conversion back
     myPedlist <- as.pedlist( myPed )   #  and forth between formats.

