getCVreplicates.child <- function(curdata, numsamp,
numreplicates, min.samp.percent, impute.bool,
missingvalue) {
newrow = {
}
# numsamp=length(curdata)
goodsamps <- 0
for (samp in seq(1, numsamp, numreplicates)) {
i = samp
j = i + numreplicates - 1
curdata_int = curdata[c(i:j)]
if (is.na(missingvalue) == TRUE) {
check_zeros = which(is.na(curdata_int) ==
TRUE)
} else {
check_zeros = which(curdata_int == missingvalue)
}
# check_zeros=which(curdata_int==0)
na_thresh = round(min.samp.percent * numreplicates)
if (length(check_zeros) >= na_thresh) {
cvval <- NA
# newrow<-cbind(newrow,cvval)
} else {
# temporarily replace the missing intensities, set
# to 0 in apLCMS, with mean intensity value of the
# corresponding replicates (with non-zero values)
if (length(check_zeros) > 0) {
if (impute.bool == TRUE) {
curdata_int[check_zeros] = mean(t(curdata_int[-c(check_zeros)]))
}
}
sdval <- sd(curdata_int)
meanval <- mean(t(curdata_int))
cvval <- 100 * (sdval/meanval)
newrow <- cbind(newrow, cvval)
goodsamps <- goodsamps + 1
}
}
if (length(newrow) > 0) {
na_ind = which(is.na(newrow) == TRUE)
if (length(na_ind) > 0) {
sumrow = summary(as.vector(newrow[-na_ind]))
} else {
sumrow = summary(as.vector(newrow))
}
} else {
sumrow <- {
}
}
if (length(sumrow) < 6) {
for (i in 1:6) {
sumrow[i] = 200
}
}
finalmat <- {
}
finalmat <- rbind(finalmat, c(unlist(sumrow),
goodsamps))
return(finalmat)
}
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