Package 'metagenomeSeq' - Bioconductor

6 correlationTestcorrectIndicesCalculate the correct indices for the output of correlationTestDescriptionUsageConsider the upper triangular portion of a matrix of size nxn. Results from the correlationTestare output as the combination of two vectors, correlation statistic and p-values. The order of theoutput is 1vs2, 1vs3, 1vs4, etc. The correctIndices returns the correct indices to fill a correlationmatrix or correlation-pvalue matrix.correctIndices(n)ArgumentsnThe number of features compared by correlationTest (nrow(mat)).ValueA vector of the indices for an upper triangular matrix.Examplesdata(mouseData)mat = MRcounts(mouseData)[55:60,]cors = correlationTest(mat)ind = correctIndices(nrow(mat))cormat = as.matrix(dist(mat))cormat[cormat>0] = 0cormat[upper.tri(cormat)][ind] = cors[,1]table(cormat[1,-1] - cors[1:5,1])correlationTestPairwise correlation for each row of a matrix or MRexperiment objectDescriptionUsageCalculates the pairwise correlation statistics and associated p-values.correlationTest(obj, method = "pearson", alternative = "two.sided",norm = TRUE, log = TRUE, parallel = FALSE, cores = 2,override = FALSE, ...)