Example data needed to run all examples contained in the documentation files of the BEclear-package
Contains a data matrix and a samples data frame which can be used to run the examples of the BEclear package.
An example data matrix that is filled with beta values originally stemming from breast cancer data from the TCGA portal , colnames are sample ids, rownames are gene names. Generally, beta values are claculated by dividing the methylated signal by the sum of the unmethylated and methylated signals from a DNA methylation microrarray. The sample data used here contains averaged beta values of probes that belong to promoter regions of single genes. Another possibility would be to use beta values of single probes, whereby the probe names should then be used instead of the gene names as rownames of the matrix.
An example data frame containing a column for the sample id and a column for the corresponding batch id.
A data frame (ex.samples) and a matrix (ex.data)
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## Not run: data(BEclearData) ## Whole procedure that has to be done to make a prediction using the BEclear ## function # Calculate median difference values and p-values meds <- calcMedians(data=ex.data, samples=ex.samples) pvals <- calcPvalues(data=ex.data, samples=ex.samples) # Summarize p-values and median differences for batch affected genes sum <- calcSummary(medians=meds, pvalues=pvals) # Set entries defined by the summary to NA clearedMatrix <- clearBEgenes(data=ex.data, samples=ex.samples, summary=sum) # Predict the missing entries with standard parameters predicted <- BEclear(data=clearedMatrix) ## End(Not run)
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