calcSummary: Summarize median comparison and p-value calculation results
In BEclear: Correction of batch effects in DNA methylation data

Description Usage Arguments Details Value See Also Examples

Summarizes the results of the calcBatchEffects function

1	calcSummary(medians, pvalues, mediansTreshold, pvaluesTreshold)

`medians`	a matrix containing median difference values calculated by the `calcBatchEffects` function. For further details look at the documentation of this function.
`pvalues`	a matrix containing p-values calculated by the `calcBatchEffects` function. For further details look at the documentation of this function.
`mediansTreshold`	the threshold above or equal median values are regarded as batch effected, when the criteria for p-values is also met.
`pvaluesTreshold`	the threshold below or equal p-values are regarded as batch effected, when the criteria for medians is also met.

calcSummary

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.table 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.

calcBatchEffects

correctBatchEffect

## 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, ]

## Calculate the batch effects
batchEffects <- calcBatchEffects(data = ex.data, samples = ex.samples,
adjusted = TRUE, method = "fdr")
med <- batchEffects$med
pvals <- batchEffects$pval

## Summarize p-values and median differences for batch affected genes
sum <- calcSummary(medians = med, pvalues = pvals)