calcMedians {BEclear}R Documentation

Calculate median difference values

Description

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.

Usage

calcMedians(data, samples, parallel=TRUE, cores=4)

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".

parallel

should the calculation be done in parallel mode? snowfall package is needed to run the function in parallel mode.

cores

if running in parallel mode, define the number of cores used for the calculation. snowfall package is needed to run the function in parallel mode

Value

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.

See Also

snowfall correctBatchEffect

Examples


## 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,]
medians <- calcMedians(data=ex.data, samples=ex.samples, parallel=FALSE)


[Package BEclear version 1.12.1 Index]