calcSummary {BEclear} | R Documentation

## 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)

[Package BEclear version 2.2.0 Index]