Description Usage Arguments Examples
Please refer to the file /inst/doc/readme.pdf.
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data |
|
dataType |
|
HG7 |
|
ERCC |
|
TN |
|
TC |
|
CR |
|
NR |
|
DESeq |
|
UQ |
|
TMM |
|
TU |
|
GAPDH |
|
nonzeroRatios |
|
cvNorm |
|
cvResolution |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 | ##---- 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 (data, dataType = c("bk", "sc"), HG7 = NULL, ERCC = NULL,
TN = NULL, TC = NULL, CR = NULL, NR = NULL, DESeq = NULL,
UQ = NULL, TMM = NULL, TU = 0, GAPDH = NULL, nonzeroRatios = c(0.7,
0.8, 0.9, 1), cvNorm = TRUE, cvResolution = 0.005)
{
grid_result <- NULL
if (length(TU) == 1 && TU == 1) {
colnames_paraMatrix <- c("nonzeroRatio", "pre_ratio",
"lower_trim", "upper_trim")
write.table(t(as.matrix(colnames_paraMatrix)), file = "bestPara.txt",
sep = "\t", row.names = FALSE, col.names = FALSE)
}
for (i in nonzeroRatios) {
if (dataType == "sc") {
if ((ncol(data) * i) <= 100) {
cat("nonzeroRatio:", i, " is too small!\n")
stop("We suggest that the minimal counts of
nonzero samples should be greater than 100!")
}
}
result <- nonzeroRatio2AUCVC(data = data, dataType = dataType,
HG7 = HG7, ERCC = ERCC, TN = TN, TC = TC, CR = CR,
NR = NR, DESeq = DESeq, UQ = UQ, TMM = TMM, TU = TU,
GAPDH = GAPDH, nonzeroRatio = i, cvNorm = cvNorm,
cvResolution = cvResolution)
nonzeroM <- matrix(i, 1, 1, TRUE)
colnames(nonzeroM) <- "NonzeroRatio"
grid_record <- cbind(nonzeroM, result)
grid_result <- rbind(grid_result, grid_record)
}
return(grid_result)
}
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