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## ----setup1, include=FALSE----------------------------------------------------
require(knitr)
## ----setup2, include=FALSE----------------------------------------------------
old_ops<-options(width=80) # make the printing fit on the page
set.seed(1121) # make the results repeatable
stdt<-date()
## ----fastJT, eval=FALSE-------------------------------------------------------
# res <- fastJT(Y, X, outTopN=15, numThreads=1, standardized=TRUE)
## ----fastJTselect, eval=FALSE-------------------------------------------------
# res <- fastJT.select(Y, X, cvMesh=NULL, kFold=10L,
# selCrit=NULL, outTopN=15L, numThreads=1L)
## ----inputPara----------------------------------------------------------------
num_sample <- 100
num_marker <- 4
num_feature <- 50
## ----markers_levels_geno_types------------------------------------------------
set.seed(12345);
Data <- matrix(rnorm(num_sample*num_marker),
num_sample, num_marker)
Feature <- matrix(rbinom(num_sample*num_feature,2,0.5),
num_sample, num_feature)
colnames(Data) <- paste0("Mrk:",1:num_marker)
colnames(Feature) <- paste0("Ftr:",1:num_feature)
## ----loadpkg------------------------------------------------------------------
library(fastJT)
## ----exp3, results='hide'-----------------------------------------------------
JTStat <- fastJT(Y=Data, X=Feature, outTopN=10)
summary(JTStat, Y2Print=1:4, X2Print=1:5)
## ----exp4, echo=FALSE, size='tiny'--------------------------------------------
summary(JTStat, Y2Print=1:4, X2Print=1:5)
## ----exp5, eval=FALSE---------------------------------------------------------
# summary(JTStat, Y2Print=1:4, X2Print=1:5, printP=FALSE)
## ----exp6, echo=FALSE, size='tiny'--------------------------------------------
summary(JTStat, Y2Print=1:4, X2Print=1:5, printP=FALSE)
## ----exp7, results='hide'-----------------------------------------------------
JTAll <- fastJT(Y=Data, X=Feature, outTopN=NA)
summary(JTAll, Y2Print=1:4, outTopN=3)
## ----exp8, echo=FALSE, size='tiny'--------------------------------------------
summary(JTAll, Y2Print=1:4, outTopN=3)
## ----select1, eval=FALSE------------------------------------------------------
# fastJT.select(Y=Data, X=Feature, cvMesh=NULL, kFold=5,
# selCrit=NULL, outTopN=5, numThreads=1)
## ----select1out, echo=FALSE, size='tiny'--------------------------------------
fastJT.select(Y=Data, X=Feature, cvMesh=NULL, kFold=5,
selCrit=NULL, outTopN=5, numThreads=1)
## ----cvMesh, results='hide'---------------------------------------------------
Mesh <- function(rownamesData, kFold){
numSamples <- length(rownamesData)
res <- NULL
subSampleSize <- floor(numSamples/kFold)
for (i in 1:kFold){
start <- (i-1)*subSampleSize + 1
if(i < kFold)
end <- i*subSampleSize
else
end <- numSamples
if(i == 1)
res <- list(c(start:end))
else
res[[i]] <- c(start:end)
}
res
}
## ----selCrit, results='hide'--------------------------------------------------
whichpart <- function(x, n=30) {
nx <- length(x)
p <- nx-n
xp <- sort(x, partial=p)[p]
which(x > xp)
}
selectCrit <- function(J, P){
pcut <- 0.95
hit <- NULL
for(i in 1:ncol(P)){
if(i == 1)
hit <- list(rownames(P)[whichpart(P[,i], 4)])
else
hit[[i]] = rownames(P)[whichpart(P[,i], 4)]
}
res <- do.call(cbind, hit)
colnames(res) <- colnames(P)
res
}
## ----select2, eval=FALSE------------------------------------------------------
# fastJT.select(Data, Feature, cvMesh=Mesh, kFold=5,
# selCrit=selectCrit, outTopN=5, numThreads=1)
## ----select2out, echo=FALSE, size='tiny'--------------------------------------
fastJT.select(Data, Feature, cvMesh=Mesh, kFold=5,
selCrit=selectCrit, outTopN=5, numThreads=1)
## ----sessinfo, echo=FALSE, include=TRUE, results='asis'-----------------------
toLatex(sessionInfo(), locale=FALSE)
## ----times, echo=FALSE, include=TRUE------------------------------------------
print(paste("Start Time",stdt))
print(paste("End Time ",date()))
## reset options
options(old_ops)
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