ped2geneSet {GeneticsBase}R Documentation

translate a ped matrix to a geneSet object

Description

Translate a ped matrix to a geneSet object.

Usage

  ped2geneSet(ped,
              markerNames,
              columns=c("family", "pid", "father", "mother",
                        "sex", "affected"),
              quiet=FALSE,
              filename)

Arguments

ped pedigree data frame whose first 6 columns are family (pedigree id), pid (patient id), father (father id), mother (mother id), sex, affected (affection status). The remaining columns are pairs of marker alleles. Each row corresponds to an individual.
markerNames names of markers
columns names of the first 5 (or 6) columns of ped file. It should be either equal to c("family","pid","father","mother"," sex","affected") or equal to c("family","pid","father","mother","sex")
quiet print intermediate results if quiet=FALSE.
filename the name of the file recording the matrix ped.

Value

geneSetObject an object of geneSet class

Author(s)

Weiliang Qiu stwxq@channing.harvard.edu, Ross Lazarus ross.lazarus@channing.harvard.edu


[Package GeneticsBase version 1.0.0 Index]