makeContMatrix {CEMiTool}R Documentation

Make a LIMMA contrast matrix

Description

Make a LIMMA contrast matrix

Usage

makeContMatrix(sample_annot, class_column = "Class",
  which_groups = "all", comp_group = "none", subject_col = NULL,
  expr)

Arguments

sample_annot

Sample annotation data.frame

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

Value

A list containing LIMMA contrast and design matrices

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]