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")

[Package MatrixQCvis version 1.0.0 Index]