fbatcStrategyStep {fbati}

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=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 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.