calcSummary {BEclear} | R Documentation |
Summarizes the results of the calcBatchEffects
function
calcSummary(medians, pvalues, mediansTreshold, pvaluesTreshold)
medians |
a matrix containing median difference values calculated by
the |
pvalues |
a matrix containing p-values calculated by the
|
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. |
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
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.
## 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)