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 1.1.2 Index]