Summarizes the results of the median comparison function
calcMedians and the p-value calculation function
calcPvalues. Should be used with the matrices originating from
these two functions.
a matrix containing median difference values calculated by
a matrix containing p-values calculated by the
All genes with a median comparison value >= 0.05 and a p-value of <= 0.01 are summarized into a data.frame. These genes are assumed to contain a batch effect
Null if there are no batch effects detected, else A data frame with the columns "gene" containing the gene name, "batch" containing the batch number from which the gene was found, "median" and "p-value" containing the calculated median difference values and the p-values, respectively.
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## Shortly running example. For a more realistic example that takes ## some more time, run the same procedure with the full BEclearData ## dataset. ## Whole procedure that has to be done to use this function. data(BEclearData) ex.data <- ex.data[31:90,7:26] ex.samples <- ex.samples[7:26,] # Calculates median difference values and p-values from the example data library(data.table) samples <- data.table(ex.samples) data <- data.table(feature=rownames(ex.data), ex.data) data <- melt(data = data, id.vars = "feature", variable.name = "sample", value.name = "beta.value") setkey(data, "feature", "sample") med <- calcMedians(data=data, samples=samples) pvals <- calcPvalues(data=data, samples=samples, adjusted=TRUE, method="fdr") # Summarize p-values and median differences for batch affected genes sum <- calcSummary(medians=med, pvalues=pvals)
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