process_data: Process Data
In famSKATRC: Family Sequence Kernel Association Test for Rare and Common Variants

Description Usage Arguments Value See Also Examples

Processes the raw data included to produce data identical to the (also included) sample.ped.geno data set. This can be used for processing your own pedigrees with SNP data.

1 2	process_data(Data = read.table(system.file("extdata", "data", package = "famSKATRC"), header = TRUE))

Data

A string, the path to the location of the data file you are processing, formatted as the included example, which can be loaded with: read.table(system.file("extdata", "data", package = "famSKATRC"), header = TRUE) and can be found in your filesystem at: system.file("extdata", "data", package = "famSKATRC")

Returns the data frame with completed preprocessing changes for famSKATRC. Mainly reworking IDs so there are not duplicates.

famSKATRC

sample.ped.geno <- process_data()
## The function is currently defined as
function(Data = read.table(system.file("extdata", "data",
                                                package = "famSKATRC"), header = TRUE))
{
  Data[ , "IID"] = paste(Data[ , "FID"]  , Data[ , "IID"]  ,sep=".")
  Data[Data[,"FA"]!=0 , "FA"] = paste(Data[Data[,"FA"]!=0 , "FID"], Data[Data[,"FA"]!=0,
                                                                        "FA"]  ,sep=".")
  Data[Data[,"FA"]!=0 , "MO"] = paste(Data[Data[,"FA"]!=0 , "FID"], Data[Data[,"FA"]!=0,
                                                                        "MO"]  ,sep=".")
  return(Data)
}