| makeContMatrix {CEMiTool} | R Documentation |
Make a LIMMA contrast matrix
makeContMatrix(sample_annot, class_column = "Class", which_groups = "all", comp_group = "none", subject_col = NULL, expr)
sample_annot |
Sample annotation |
class_column |
Character string indicating the sample grouping column. Default: "Class" |
which_groups |
Optional character vector to use if selecting groups to be compared (e.g. disease1, disease3, but not disease2) |
comp_group |
Optional character string indicating group to compare groups against. If "none" (the default), compares all groups against each other. |
subject_col |
Optional character string indicating a column containing subject information |
expr |
Optional expression matrix for direct compatibility with makeLimmaComp |
A list containing LIMMA contrast and design matrices
## 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)