ECDF {MatrixQCvis} | R Documentation

## Create ECDF plot of a sample against a reference

### Description

The function 'ECDF' creates a plot of the empirical cumulative distribution function of a specified sample and an outgroup (reference). The reference is specified by the 'group' argument. The row-wise (feature) mean values of the reference are calculated after excluding the specified 'sample'.

### Usage

    ECDF(se, sample = colnames(se), group = c("all", colnames(colData(se))))

### Arguments

`se` | 'SummarizedExperiment' object
`sample` | 'character', name of the sample to compare against the group
`group` | 'character', either '"all"' or one of 'colnames(colData(se))'

### Details

Internal use in 'shinyQC'.

### Value

'gg' object from 'ggplot2'

### Examples

    ## create se
    set.seed(1)
    a <- matrix(rnorm(1000), nrow = 100, ncol = 10,
        dimnames = list(1:100, paste("sample", 1:10)))
    a[c(1, 5, 8), 1:5] <- NA
    cD <- data.frame(name = colnames(a), type = c(rep("1", 5), rep("2", 5)))
    rD <- data.frame(spectra = rownames(a))
    se <- SummarizedExperiment(assay = a, rowData = rD, colData = cD)

    ECDF(se, sample = "sample 1", group = "all")

[Package MatrixQCvis version 1.2.4 Index]