What the package does (short line)

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Documentation for package `geneProspData' version 1.0

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geneProspData-package What the package does (short line) ~~ package title ~~
applyAddGenoSignal calculate the magnitude of the linear effect of an additive signal given one subject's genotypic covariates for all blocks.
applyAddSignal calculate the magnitude of the linear effect of an additive signal given one subject's haplotype block indexes for all blocks.
applyGenoSignalRules calculate the magnitude of the effect of all signals given one subject's haplotype block indexes for all blocks.
applyInActGenoSignal calculate the magnitude of the effect of an interactive signal given one subject's genotypic covaraites for all blocks.
applyInActSignal calculate the magnitude of the effect of an interactive signal given one subject's haplotype block indexes for all blocks.
applySignalRules calculate the magnitude of the effect of all signals given one subject's haplotype block indexes for all blocks.
applySingleLocusSignal2Dip calculate whether the two haplotypes carry disease signal. If at least one carry, the effect is at most the value defined in the signal
applySRule2Dip calculate whether the two haplotypes carry disease signal. If at least one carry, the effect is at most the value defined in the signal
calSignalEffect calculate the probability of getting disease given ones agreement with signal rules, identified by 0/1 boolean matrix
caseControlAssigner Decide a binary outcome based on the risk probability.
constructTreeDFrame reconstruct the data.frame object so it can be used by the regression function rpart()
df.sampleBkMap randomly sampled a fixed number of blocks from a matrix which contained haplotype block info
df.selBkMap reconstruct the object of bkMap so that its key has the same order as the keyVal
geneProspData What the package does (short line) ~~ package title ~~
genoSignalRuleContr constructor of the genoSignalRule object.
getVarIndex find out the ith to jth loci the current block covers
hapBk2AlleleSeq convert a matrix of binary expression for multiple subjects into a matrix of 0/1
mapSignalRule create a literal expression of the signal rule
match1AddSignal check whether the subject has the block index defined in the additive rule, which has only one index
matchInActSignal check whether the subject has all the block indexes defined in the interaction rule.
matchMultipleLocusSignal check whether the subject has all the binary expression index matching the one defined in genoSignalRule
matchSingleLocusSignal check whether the subject has the binary expression index matching the one defined in genoSignalRule
sampleFromBkMap sample binary expressions for selected blocks
sampleGenoSigns sample the binary code in each signal-carrying genotypic covariate
sampleSigns sample the index of binary expression in each signal-carrying block
signalContr constructor of the signal object.
signalRule.2singleLocusRule reconstruct the signal rule from the one define on the block to the one defined on a single loci on the block, replace the block index with index in the whole haplotype sequence and update whether the data on the loci is 0/1
signalRuleContr cosntruct the signal rule
updateBlockBinaFreq update the existing bkMap with the frequency for one block's binary expression re-allocated
writeDframe recode the data.frame as factor and as numerica for CART and GLM to use. Also may write the data.frame as a .csv file.