gatherCors: gatherCors

In NormExpression: Normalize Gene Expression Data using Evaluated Methods

gatherCors

Description

Please refer to the file /inst/doc/readme.pdf.

Usage

gatherCors(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)

Arguments

data	Please refer to the file /inst/doc/readme.pdf.
cor_method	Please refer to the file /inst/doc/readme.pdf.
HG7	Please refer to the file /inst/doc/readme.pdf.
ERCC	Please refer to the file /inst/doc/readme.pdf.
TN	Please refer to the file /inst/doc/readme.pdf.
TC	Please refer to the file /inst/doc/readme.pdf.
CR	Please refer to the file /inst/doc/readme.pdf.
NR	Please refer to the file /inst/doc/readme.pdf.
DESeq	Please refer to the file /inst/doc/readme.pdf.
UQ	Please refer to the file /inst/doc/readme.pdf.
TMM	Please refer to the file /inst/doc/readme.pdf.
TU	Please refer to the file /inst/doc/readme.pdf.
GAPDH	Please refer to the file /inst/doc/readme.pdf.
pre_ratio	Please refer to the file /inst/doc/readme.pdf.
lower_trim	Please refer to the file /inst/doc/readme.pdf.
upper_trim	Please refer to the file /inst/doc/readme.pdf.
rounds	Please refer to the file /inst/doc/readme.pdf.

Examples

##---- 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)
  }

NormExpression documentation built on May 29, 2024, 2 a.m.