hoeffDValues {MatrixQCvis}

R Documentation

Create values of Hoeffding's D statistics from M and A values

Description

The function creates and returns Hoeffding's D statistics values from MA values.

Usage

hoeffDValues(tbl, name = "raw")

Arguments

tbl	'tibble', as obtained from the function 'MAvalues'
name	'character', name of the returned list

Details

The function uses the function 'hoeffd' from the 'Hmisc' package to calculate the values.

Value

named list with Hoeffding's D values per sample

Examples

## 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")

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