fbat {fbat}R Documentation

Family-Based Association Tests

Description

Family-Based Assoiciation Tests for biallelic markers.

Usage

  fbat(geneSetObj, 
       model="a", 
       traitMethod=3, 
       traitOffset=0, 
       quiet=TRUE)

  fbat.default(pedObj, 
               model="a", 
               traitMethod=3, 
               traitOffset=0, 
               quiet=TRUE)

Arguments

geneSetObj an object of geneSet.
pedObj a list with five elements: ped, columns, markerNames, Position, and filename. ped is a 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; columns are the 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"); founderOnly indicates if using only founder info; markerNames is a vector of marker names; Position is a vector of marker positions; fileName is the pedigree file name
model Genotype coding method. model="d" means GDOM (dominante) coding; model="r" means GREC (recessive) coding; model="g" means GEN (genotype) coding; model="a" or otherwise means GTDT (additive) coding.
traitMethod Trait coding method. traitMethod=1 means T=y-offset, where y is the trait and offset is an offset. In a .ped file, y=2 if affected; y=1 if unaffected; and y=0 if unknown. traitMethod=2 means T=1 if affected, T=0 otherwise.
traitOffset Offset if traitMethod=1.
quiet Print some intermediate results if quiet=FALSE.

Value

statPvalue A m by 3 matrix with the 3 columns: test statistics, degree of freedom and pvalues, where m is the number of markers.
S.list A list of S scores for markers.
ES.list A list of expected S scores for markers.
CovS.list A list of covariance matrix of S scores for markers.
alleles.list A list of alleles for markers
familySize size of nuclear families
flagMarkers A vector of flags. flagMarkers[i]=1 if for marker i, all children genotypes in all families are missing. Otherwise flagMarkers[i]=0.
numInfoFamily number of informative families at each marker

Author(s)

Weiliang Qiu stwxq@channing.harvard.edu, Ross Lazarus ross.lazarus@channing.harvard.edu, Gregory Warnes warnes@bst.rochester.edu, Nitin Jain nitin.jain@pfizer.com

References

Horvath et al. The family based association test method: computing means and variances for general statistics. Technical report http://www.biostat.harvard.edu/~fbat/fbattechreport.ps.

Rabinowitz and Laird (2000). A Unified Approach to Adjusting Association Tests for Population Admixture with Arbitrary Pedigree Structure and Arbitrary Missing Marker Information. Human Heredity 50:211-223.

Laird et al. (2000). Implementing a Unified Approach to Family-Based Tests of Association. Genetic Epidemiology 19(Suppl 1):S36-S42.

Schaid (1996). General Score Tests for Associations of Genetic Markers With Disease Using Cases and Their Parents. Genetic Epidemiology 13:423-449.

Examples

  data(CAMP)
  tmp<-fbat(CAMP)
  summaryPvalue(tmp)

[Package fbat version 1.2.0 Index]