lm2Contrast: Linear Model analysis with limma
In spell098/rnaseq_app:

Description Usage Arguments Value Author(s) See Also Examples

Linear Model analysis with limma

1	lm2Contrast(expr.matrix, design)

`expr.matrix`	A matrix of standardized data. Columns = samples, rows = genes,transcripts,CpG...
`design`	The design of the experiment (object)

Linear model contrast ...

lm2.contrast: MArrayLM object(limma) result of the eBayes function.
contrasts: Vector of contrasts
contrast.matrix: Matrix of contrasts

Simon J Pelletier

design_contrasts makeContrasts lmFit MArrayLM

expr.matrix <- readRDS("data/expr_matrix_LGVD.rds")
design <- design_contrasts(get_names(colnames(expr.matrix)))
results_list <- results_topTable()
lm2 <- lm2Contrast(expr.matrix,design)
lm2.contrast = lm2[[1]]
contrasts=lm2[[2]]
contrast.matrix=lm2[[3]]