hoeffDValues {MatrixQCvis} | R Documentation |
The function creates and returns Hoeffding's D statistics values from MA values.
hoeffDValues(tbl, name = "raw")
tbl |
'tibble', as obtained from the function 'MAvalues' |
name |
'character', name of the returned list |
The function uses the function 'hoeffd' from the 'Hmisc' package to calculate the values.
named list with Hoeffding's D values per sample
## create se a <- matrix(1:100, nrow = 10, ncol = 10, dimnames = list(1:10, paste("sample", 1:10))) a[c(1, 5, 8), 1:5] <- NA set.seed(1) a <- a + rnorm(100) cD <- data.frame(name = colnames(a), type = c(rep("1", 5), rep("2", 5))) rD <- data.frame(spectra = rownames(a)) se <- SummarizedExperiment::SummarizedExperiment(assay = a, rowData = rD, colData = cD) tbl <- MAvalues(se) hoeffDValues(tbl, "raw") ## normalized values se_n <- se assay(se_n) <- normalizeAssay(a, "sum") tbl_n <- MAvalues(se_n, group = "all") hoeffDValues(tbl_n, "normalized") ## transformed values se_t <- se assay(se_t) <- transformAssay(a, "log2") tbl_t <- MAvalues(se_t, group = "all") hoeffDValues(tbl_t, "transformed")