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.
fbatcStrategyStepUp(ped, phe, markers=pedMarkerNames(ped), trait="trait",
traitType="auto", alphaMMarker=0.05, alphaStep=alphaMMarker, sortByCorrelation=TRUE,
tempPrefix="temp_", sim=FALSE, debug=FALSE )
fbatcStrategyStepDown(ped, phe, markers=pedMarkerNames(ped),
markersChosen=pedMarkerNames(ped), markersChosenR=markersChosen, trait="trait",
traitType="auto", alphaMMarker=0.05, alphaStep=alphaMMarker, sortByCorrelation=TRUE,
tempPrefix="temp_", sim=FALSE, debug=FALSE )
fbatcStrategyStep(ped, phe, markers=pedMarkerNames(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 fbatcSStep
print(x,...)
Object from (f)read.ped or as.ped. See write.ped in the pbatR R package for more details on the file format.
Object from (f)read.phe or as.phe. See write.phe in the pbatR R package for more details on the file format.
Names of the markers to analyze.
Name of the trait to analyze. Can be dichotomous or continuous.
"auto","dichotomous", or "continuous". If "auto" (the default), then "dichotomous" will be set if there are only two levels of the phenotype.
Alpha value for the multimarker test.
Alpha value used in the stepwise procedure.
Whether to sort the markers by putting those in highest correlation closest to each other.
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.
Developer use only.
Result of 'fbatcStrategyStep' routine.
Number of significant digits to display.
If set to a filename, then the output is redirected to that file instead of the standard output.
Whether to produce a latex file that can be compiled, or only the code for the chart.
Whether to run pdflatex on the file (requires preamble=TRUE), pdflatex must be in your path (generally true in linux, but not in Windows).
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.
In the step-down approach, the markers to start with for the model-based approach.
In the step-down approach, the markers to start with for the model-free approach.
Developer use only.
Result of fbatcStrategyStep, fbatcStrategyStepUp, fbatcStrategyStepDown.
Extra arguments.
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.