countValuesToPredict: Count NA entries in a matrix
In BEclear: Correction of batch effects in DNA methylation data

Description Usage Arguments Details Value See Also Examples

Simple function that counts all values in a matrix which are NA

1	countValuesToPredict(data)

data

any kind of matrix

countValuesToPredict

Returns a data frame with the number of NA entries per column. Since the function is mainly written for the usage in batch effect correction of DNA methylation data, the column names of the data frame are set to "sample" and "num_pred_values". Nevertheless, the function can be used with any other matrix containing anything but beta values.

clearBEgenes

BEclear

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")
meds <- batchEffects$med
pvals <- batchEffects$pval

## Summarize p-values and median differences for batch affected genes
sum <- calcSummary(medians = meds, pvalues = pvals)
clearedMatrix <- clearBEgenes(data = ex.data, samples = ex.samples, summary = sum)
numberOfEntries <- countValuesToPredict(data = clearedMatrix)