calcSummary: Summarize median comparison and p-value calculation results

In uds-helms/BEclear: Correction of batch effects in DNA methylation data

Summarize median comparison and p-value calculation results

Description

Summarizes the results of the calcBatchEffects function

Usage

calcSummary(medians, pvalues, mediansTreshold, pvaluesTreshold)

Arguments

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.

Details

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

Value

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.

See Also

calcBatchEffects

correctBatchEffect

Examples

## 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)

uds-helms/BEclear documentation built on April 16, 2023, 12:44 a.m.