Summarize median comparison and p-value calculation results
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
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 med <- calcMedians(data=ex.data, samples=ex.samples, parallel=FALSE) pvals <- calcPvalues(data=ex.data, samples=ex.samples, parallel=FALSE, adjusted=TRUE, method="fdr") # Summarize p-values and median differences for batch affected genes sum <- calcSummary(medians=med, pvalues=pvals)
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