power: Power And Sample Size Calculations

Description

Does power and sample size calculations. Note that this may be very highly pbat version specific, and more finicky than other methods in this package, as it requires that the menuing interface does not change.

The Windows version requires a slight hack to control PBAT, which appears to be stable, but may have a race condition on heavily loaded systems. Unix/Linux users should not encounter this.

'pbat.power()' starts the GUI interface (strongly recommended) 'pbat.binaryFamily(...)' is for family based designs with binary 'pbat.continuous(...)' is for family based designs with continuous 'pbat.caseControl(...)' is for case/control designs 'pbat.popQuant(...)' is for population designs with quantitative Currently less extensive range checking is done in these routines unlike the rest of the routines in pbatR.

Usage

pbat.power()
pbat.binaryFamily(
           numOffspring=1, missingParents=0, numFam=0,
           addiOffspringPheno=1, ## only when you have missing parents
           ascertainment="unaffected",
           model="additive", model.afreq=0.2, model.incrAfreq=0,
           model.disLocIsMarker=TRUE,
           
           model.popPrev=NULL,  ## Options 1, 3, & 4
           model.genAF=NULL,    ## Option 1
           model.penAA=NULL, model.penAB=NULL, model.penBB=NULL, ## Option 2
           model.OR=NULL,       ## Option 3
           model.aOR=NULL,      ## Option 4
           
           stat.sigLevel=0.01,
           stat.offset="",  ## defaults to population prevalence
           comp="numerical",
           log="pbatLog.txt")
pbat.continuousFamily(
           numOffspring=1, missingParents=0, numFam=0,
           addiOffspringPheno, ## only when you have missing parents
           ascertainment="unaffected",
           model="additive", model.afreq=0.1, model.incrAfreq=0,
           model.disLocIsMarker=FALSE,                      
           model.heritability=0.1, model.afreqMarker=0,
           model.prDiseaseGivenMarker=1,
           stat.sigLevel=0.05, stat.offset="",
           comp="numerical",
           log="pbatLog.txt")
pbat.caseControl(
           model="additive", model.minafreq=0.1, model.incrAfreq=0.1,
           model.prevalence=0.1,
           model.ORofABvsBB=NULL, # Option 1 - default 1.5
           model.aOR=NULL,      # Option 2 - default 1.481
           comp.cases=500, comp.controls=500, comp.caseControlRatio=1.5,
           comp.power=0.8, comp.sigLevel=0.05, comp.numSim=1000,
           mode="power",
           log="pbatLog.txt")
pbat.popQuant(
           model="additive",
           model.minafreq=0.2, model.incrAfreq=0.1,
           model.heritability=0.001,
           comp.numProbands=2000,
           comp.power=0.8, comp.sigLevel=0.05, comp.numSim=10000,
           mode="power",
           log="pbatLog.txt")

Arguments

numOffspring

Family - number of offspring

missingParents

Family - number of missing parents (0,1,2)

numFam

Family - number of families

addiOffspringPheno

Only used when you have missing parents; additional offspring phenotypes. 1 for yes, 0 for no.

ascertainment

'unaffected', 'affected', or 'not applicable'

model

'additive', 'dominant', 'recessive' or (only for binary / case control) 'multi'

model.afreq

allele frequency

model.incrAfreq

increment allele frequency

model.disLocIsMarker

TRUE/FALSE - whether the disease locus is the same as the marker locus

model.popPrev

population prevalence

model.prevalence

population prevalence

model.genAF

genetic attributable fraction of the gene

model.penAA

penetrance of AA genotype

model.penAB

penetrance of AB genotype

model.penBB

penetrance of BB genotype

model.OR

odds ratio

model.aOR

allelic odds ratio

model.heritability

heritibility

model.afreqMarker

marker allele frequency

model.prDiseaseGivenMarker

Pr(Disease|marker)

model.ORofABvsBB

odds ratio of AB to BB

model.minafreq

minimum allele frequency

stat.sigLevel

significance level

stat.offset

offset; defaults to population prevalence

comp

'numerical':numerical integration, 'approximation':approximation, 'simulation':simulation

comp.cases

number of cases

comp.controls

number of controls

comp.caseControlRatio

case control ratio

comp.power

power

comp.sigLevel

significance level

comp.numSim

number of simulations to run

comp.numProbands

number of probands

mode

'power' for power result given parameter specification, 'ss' for sample size result given parameter specification; note that not all parameters will be used for 'power' and 'ss'.

log

logfile to write to (results will be stored here) - this will be over-written if the file exists

References

http://www.biostat.harvard.edu/~clange/default.htm http://www.people.fas.harvard.edu/~tjhoffm/pbatR.html

Description

Usage

Arguments

References

See Also