ECDF {MatrixQCvis} | R Documentation |
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'.
ECDF(se, sample = colnames(se), group = c("all", colnames(colData(se))))
se |
'SummarizedExperiment' object |
sample |
'character', name of the sample to compare against the group |
group |
'character', either '"all"' or one of 'colnames(colData(se))' |
Internal use in 'shinyQC'.
'gg' object from 'ggplot2'
## 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")