fbatcStrategyStep {fbati} | R Documentation |
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=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,...)
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. |
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
.