Description Usage Arguments Examples
Please refer to the file /inst/doc/readme.pdf.
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data |
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cor_method |
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HG7 |
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ERCC |
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TN |
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TC |
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CR |
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NR |
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DESeq |
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UQ |
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TMM |
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TU |
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GAPDH |
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pre_ratio |
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lower_trim |
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upper_trim |
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rounds |
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 | ##---- 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, cor_method = c("spearman", "pearson", "kendall"),
HG7 = NULL, ERCC = NULL, TN = NULL, TC = NULL, CR = NULL,
NR = NULL, DESeq = NULL, UQ = NULL, TMM = NULL, TU = NULL,
GAPDH = NULL, pre_ratio = 0.5, lower_trim = 0.05, upper_trim = 0.65,
rounds = 1e+06)
{
methodsList <- list(HG7 = HG7, ERCC = ERCC, TN = TN, TC = TC,
CR = CR, NR = NR, DESeq = DESeq, UQ = UQ, TMM = TMM,
TU = TU, GAPDH = GAPDH)
specifiedMethods <- methodsList[!unlist(lapply(methodsList,
is.null))]
numMethod <- length(specifiedMethods)
method_range <- seq(1, numMethod, 1)
ubq_genes <- identifyUbq(data, pre_ratio = pre_ratio, lower_trim = lower_trim,
upper_trim = upper_trim, min_ubq = 100)
cor_value_method <- NULL
for (j in method_range) {
norm.matrix <- getNormMatrix(data, specifiedMethods[[j]])
dataUse2Cor <- norm.matrix[ubq_genes, ]
cor.result <- getCor(dataUse2Cor, method = cor_method,
rounds = rounds)
cor_vm <- cbind(cor.result, rep(names(specifiedMethods)[j],
times = round(rounds)))
cor_value_method <- rbind(cor_value_method, cor_vm)
}
colnames(cor_value_method) <- c("Value", "Methods")
return(cor_value_method)
}
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