extractComb {MatrixQCvis} | R Documentation |
The function 'extractComb' extracts the features that match a 'combination' depending if the features was measured or missing. The function will return the sets that match the 'combination', thus, the function might be useful when answering questions about which features are measured/missing under certain combinations (e.g. sample types or experimental conditions).
extractComb(se, combination, measured = TRUE, category = "type")
se |
'SummarizedExperiment' |
combination |
'character', refers to factors in 'category' |
measured |
'logical' |
category |
'character', corresponding to a column name in 'colData(se)' |
The function 'extractComb' uses the 'make_comb_mat' function from 'ComplexHeatmap' package.
'character'
## 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) extractComb(se, combination = "2", measured = TRUE, category = "type")