calcMedians {BEclear} | R Documentation |
Compares the median value of all beta values belonging to one batch with the median value of all beta values belonging to all other batches. Returns a matrix containing this median difference value for every gene in every batch, columns define the batch numbers, rows the gene names.
calcMedians(data, samples, BPPARAM=bpparam())
data |
a |
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". |
BPPARAM |
An instance of the
|
calcMedians
a matrix containing median comparison values for all genes in all batches, the column names define the batch numbers, row names are the same gene names as contained in the input matrix.
## Shortly running example. For a more realistic example that takes ## some more time, run the same procedure with the full BEclearData ## dataset. ## Calculate median comparison values in non-parallel mode data(BEclearData) ex.data <- ex.data[31:90,7:26] ex.samples <- ex.samples[7:26,] library(data.table) samples <- data.table(ex.samples) data <- data.table(feature=rownames(ex.data), ex.data) data <- melt(data = data, id.vars = "feature", variable.name = "sample", value.name = "beta.value") setkey(data, "feature", "sample") medians <- calcMedians(data=data, samples=samples)