Description Usage Arguments Examples
Please refer to the file /inst/doc/readme.pdf.
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data |
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methods |
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HG7.size |
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ERCC.size |
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TN.size |
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TC.size |
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CR.size |
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NR.size |
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pre_ratio |
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lower_trim |
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upper_trim |
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min_ubq |
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 38 39 40 41 42 43 44 45 46 47 48 49 50 | ##---- 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, methods = c("HG7", "ERCC", "TN", "TC", "CR",
"NR", "DESeq", "UQ", "TMM", "TU"), HG7.size = NULL, ERCC.size = NULL,
TN.size = NULL, TC.size = NULL, CR.size = NULL, NR.size = NULL,
pre_ratio = 0.5, lower_trim = 0.05, upper_trim = 0.65, min_ubq = 100)
{
method1 <- as.list(methods)
numMethod <- length(method1)
method_range <- seq(1, numMethod, 1)
for (i in method_range) {
if (method1[[i]] == "HG7" || method1[[i]] == "ERCC" ||
method1[[i]] == "TN" || method1[[i]] == "TC" || method1[[i]] ==
"CR" || method1[[i]] == "NR") {
size.name <- paste(method1[[i]], ".size", sep = "")
out.name1 <- paste(method1[[i]], ".factors", sep = "")
if (is.null(size.name)) {
stop("Please provide", size.name, "!")
}
else {
assign(out.name1, getFactors(data, method = "sizefactor",
lib.size = get(size.name)))
}
}
if (method1[[i]] == "DESeq" || method1[[i]] == "RLE" ||
method1[[i]] == "UQ" || method1[[i]] == "TMM") {
out.name2 <- paste(method1[[i]], ".factors", sep = "")
assign(out.name2, getFactors(data, method = method1[[i]]))
}
if (method1[[i]] == "TU") {
TU.factors <- getFactors(data, method = "TU", pre_ratio = pre_ratio,
lower_trim = lower_trim, upper_trim = upper_trim,
min_ubq = min_ubq)
}
}
factors.list <- NULL
for (m in methods) {
m.factors <- paste(m, ".factors", sep = "")
factors.list <- c(factors.list, m.factors)
}
factors.result <- NULL
for (i in method_range) {
factors.result <- cbind(factors.result, get(factors.list[i]))
}
colnames(factors.result) <- methods
return(factors.result)
}
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