Description Usage Arguments Details Value See Also Examples
Summarizes the results of the median comparison function
calcMedians
and the pvalue calculation function
calcPvalues
. Should be used with the matrices originating from
these two functions.
1  calcSummary(medians, pvalues)

medians 
a matrix containing median difference values calculated by
the 
pvalues 
a matrix containing pvalues calculated by the

calcSummary
All genes with a median comparison value >= 0.05 and a pvalue 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 frame with the columns "gene" containing the gene name, "batch" containing the batch number from which the gene was found, "median" and "pvalue" containing the calculated median difference values and the pvalues, respectively.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22  ## 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,]
# Calculates median difference values and pvalues from the example data
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")
med < calcMedians(data=data, samples=samples)
pvals < calcPvalues(data=data, samples=samples, adjusted=TRUE,
method="fdr")
# Summarize pvalues and median differences for batch affected genes
sum < calcSummary(medians=med, pvalues=pvals)

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