makeLimmaComp {CEMiTool} | R Documentation |
Make LIMMA comparisons
makeLimmaComp(expr, design, cont.matrix)
expr |
Expression |
design |
Design matrix |
cont.matrix |
Contrast matrix |
A list with one data.frame per comparison
## Not run: # Create a mock expressionset to test functions mockexpset <- matrix(rnorm(15000), ncol = 15) colnames(mockexpset) <- paste0('GSM', seq(1, 15)) set.seed(100) rownames(mockexpset) <- apply(replicate(n = 1000, sample(letters, 8)), 2, function(x) paste(x, collapse = '')) sample_annot <- data.frame(geo_accession = colnames(mockexpset), group = c(rep('skin_healthy', 5), rep('degree1', 5), rep('degree2', 5)), subject = paste0('S', c(rep(1:5),rep(1:5), rep(1:5)))) # Testing function below # Paired cont_mat1 <- makeContMatrix(class_column = 'group', which_groups = c('degree1', 'degree2'), comp_group = 'skin_healthy', subject_col= 'subject', sample_annot = sample_annot, expr = mockexpset) limma_result1 <- do.call(makeLimmaComp, cont_mat1) # Unpaired cont_mat2 <- makeContMatrix(class_column = 'group', which_groups = c('degree1', 'degree2'), comp_group = 'skin_healthy', sample_annot = sample_annot, expr = mockexpset) limma_result2 <- do.call(makeLimmaComp, cont_mat2) ## End(Not run)