makeLimmaComp {CEMiTool} | R Documentation

## Make LIMMA comparisons

### Description

Make LIMMA comparisons

### Usage

    makeLimmaComp(expr, design, cont.matrix)

### Arguments

`expr` | Expression
`design` | Design matrix
`cont.matrix` | Contrast matrix

### Value

A list with one data.frame per comparison

### Examples

    ## 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)

[Package CEMiTool version 1.6.11 Index]