localMPR {MPR} | R Documentation |
~~ A concise (1-5 lines) description of what the function does. ~~
localMPR(baseData, allele.matrix = NULL, maxIterate = 50, returnNumIterate = FALSE, maxNStep = 5, verbose = FALSE, strEND = "\n", ...)
baseData |
~~Describe baseData here~~ |
allele.matrix |
~~Describe allele.matrix here~~ |
maxIterate |
~~Describe maxIterate here~~ |
returnNumIterate |
~~Describe returnNumIterate here~~ |
maxNStep |
~~Describe maxNStep here~~ |
verbose |
~~Describe verbose here~~ |
strEND |
~~Describe strEND here~~ |
... |
~~Describe ... here~~ |
~~ If necessary, more details than the description above ~~
~Describe the value returned If it is a LIST, use
comp1 |
Description of 'comp1' |
comp2 |
Description of 'comp2' |
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~~further notes~~
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~~objects to See Also as help
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##---- Should be DIRECTLY executable !! ---- ##-- ==> Define data, use random, ##-- or do help(data=index) for the standard data sets. ## The function is currently defined as function (baseData, allele.matrix = NULL, maxIterate = 50, returnNumIterate = FALSE, maxNStep = 5, verbose = FALSE, strEND = "\n", ...) { if (is.null(allele.matrix)) allele.matrix <- base2Allele(baseData) if (nrow(baseData) == ncol(allele.matrix)) allele.matrix <- t(allele.matrix) if (nrow(baseData) != nrow(allele.matrix)) stop("nrow(baseData)!=nrow(allele.matrix), allele.matrix error!!!") newALLELE <- ALLELE <- allele.matrix genoData <- base2Geno(baseData, allele.matrix) newRSum <- oriRSum <- length(baseData) numStepSize <- 1 numIterate <- 0 while (numStepSize <= maxNStep) { numIterate <- numIterate + 1 if (verbose) cat("\r", numIterate, "\t", newRSum, "\t", numStepSize, "\n") oriRSum <- newRSum loopRes <- .loopMPR(genoData, allele.matrix = ALLELE, numStep = numStepSize) newRSum <- loopRes[[1]] if (oriRSum > newRSum) { ALLELE <- loopRes[[2]] genoData <- loopRes[[3]] numStepSize <- 1 } else { numStepSize <- numStepSize + 1 } } if (verbose) cat("\tDone.", strEND) rownames(ALLELE) <- rownames(baseData) if (returnNumIterate) list(allele = ALLELE, num_iterate = numIterate, numR = newRSum) else ALLELE }