fbatcStrategyStep: FBAT-C Stepwise Strategy

In fbati: Gene by Environment Interaction and Conditional Gene Tests for Nuclear Families

FBAT-C Stepwise Strategy

Description

Apply the FBAT-C test in a stepwise fashion using fbatcStrategyStep (which does forward selection with fbatcStrategyStepUp, followed by backwards selection with fbatcStrategyStepDown) and get the results ready for publication with fbatcStrategyStepLatex.

Usage

fbatcStrategyStepUp(ped, phe, markers=ped.markerNames(ped), trait="trait",
  traitType="auto", alphaMMarker=0.05, alphaStep=alphaMMarker, sortByCorrelation=TRUE,
  tempPrefix="temp_", sim=FALSE, debug=FALSE )
fbatcStrategyStepDown(ped, phe,  markers=ped.markerNames(ped),
  markersChosen=ped.markerNames(ped), markersChosenR=markersChosen, trait="trait",
  traitType="auto", alphaMMarker=0.05, alphaStep=alphaMMarker, sortByCorrelation=TRUE,
  tempPrefix="temp_", sim=FALSE, debug=FALSE )
fbatcStrategyStep(ped, phe, markers=ped.markerNames(ped), trait="trait",
  traitType="auto", alphaMMarker=0.05, alphaStep=alphaMMarker, sortByCorrelation=TRUE,
  tempPrefix="temp_", sim=FALSE, debug=FALSE )
fbatcStrategyStepLatex(res, digits=4, ffile="", preamble=FALSE, build=preamble, pdf="")
## S3 method for class 'fbatcSStep'
print(x,...)

Arguments

ped	Object from (f)read.ped or as.ped. See write.ped in the pbatR R package for more details on the file format.
phe	Object from (f)read.phe or as.phe. See write.phe in the pbatR R package for more details on the file format.
markers	Names of the markers to analyze.
trait	Name of the trait to analyze. Can be dichotomous or continuous.
traitType	"auto","dichotomous", or "continuous". If "auto" (the default), then "dichotomous" will be set if there are only two levels of the phenotype.
alphaMMarker	Alpha value for the multimarker test.
alphaStep	Alpha value used in the stepwise procedure.
sortByCorrelation	Whether to sort the markers by putting those in highest correlation closest to each other.
tempPrefix	The prefix to use for some intermittent files. Changing this is only necessary when you want to run this routine in parallel when each process shares the same disk.
sim	Developer use only.
res	Result of 'fbatcStrategyStep' routine.
digits	Number of significant digits to display.
ffile	If set to a filename, then the output is redirected to that file instead of the standard output.
preamble	Whether to produce a latex file that can be compiled, or only the code for the chart.
build	Whether to run pdflatex on the file (requires preamble=TRUE), pdflatex must be in your path (generally true in linux, but not in Windows).
pdf	Name of the pdf viewer executable, if you also want to open the compiled file immediately. Note that in this case, you may not be able to return to the R session until you close this window.
markersChosen	In the step-down approach, the markers to start with for the model-based approach.
markersChosenR	In the step-down approach, the markers to start with for the model-free approach.
debug	Developer use only.
x	Result of fbatcStrategyStep, fbatcStrategyStepUp, fbatcStrategyStepDown.
...	Extra arguments.

Details

fbatcStrategy returns a list with the following components.

mmarkerPvalue: p-value of the multi-marker test on those markers (Rakovski et. al 2008).

correlation: correlation matrix of the markers

univariate: univariate results

step: (model-based test) list of components pvalue (ith pvalue of the conditional test of markersAnalyze[i] on all markersCondition), numInf (number of informative families in the ith test), markersAnalyze, and markersCondition

markersChosen: (model-based test) results from applying step-up strategy

stepR, markersChosenR: (model-free test) results similar to step and markersChosen.

fbati documentation built on Feb. 16, 2023, 9:31 p.m.