clearBEgenes: Prepare a data matrix for the BEclear function

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

Prepare a data matrix for the BEclear function

Description

A function that simply sets all values to NA which were previously found by median value comparison and p-value calculation and are stored in a summary. The summary defines which values in the data matrix are set to NA.

Usage

clearBEgenes(data, samples, summary)

Arguments

data	any matrix filled with beta values, column names have to be sample_ids corresponding to the ids listed in "samples", row names have to be gene names.
samples	data frame with two columns, the first column has to contain the sample numbers, the second column has to contain the corresponding batch number. Colnames have to be named as "sample_id" and "batch_id".
summary	a summary data.frame containing the columns "gene", "batch", "median" and "p-value" and consists of all genes which were found in the median and p-value calculations, see calcSummary function for more details.

Details

clearBEgenes

All entries belonging to genes stated in the summary are set to NA for the corresponding batches in the data matrix. Please look at the descriptions of calcBatchEffects for more detailed information about the data which should be contained in the summary data.frame.

Value

A data matrix with the same dimensions as well as the same column and row names as the input data matrix is returned, all entries which are defined in the summary are now set to NA.

See Also

calcBatchEffects

calcSummary

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

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

## Set values for summarized BEgenes to NA
clearedMatrix <- clearBEgenes(data = ex.data, samples = ex.samples, summary = sum)

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