differential expression analysis
dea(x, y, is.log = T, cutoff.fc = 2, cutoff.p = 0.01, adjust.method = unique(c("BH", stats::p.adjust.methods)), sortBy = c("fc", "p", "none"), returnValue = c("fc", "p", "all"), returnAllGenes = FALSE)
| x | matrix or character vector with matrix column names |
|---|---|
| y | matrix to compare against or matrix with x and y column names |
| is.log | is the expression data in log2 space? Default: T |
| cutoff.fc | numeric value for fold change gene cutoffs (not in log space) or NULL. Default: 2 |
| cutoff.p | numeric value for p-value gene cutoffs (not in log space) or NULL. Default: 0.01 |
| adjust.method | correction for multiple testing? 'none' if not desired. Default: unique(c("BH", stats::p.adjust.methods)) |
| sortBy | parameter to sort the genes returned by. One of fold change (default), p-value or none, in which case the original order of the rows in the matrix is kept. Default: c("fc", "p", "none") |
| returnValue | parameter describing the genes to be returned. One of fold change (default), p-value or all, in which case fold changes, p-values and genes considered 'DE' (ie if cutoffs are provided) are returned.Default: c("fc", "p", "all") |
| returnAllGenes | should all genes be returned instead of only those passing cutoffs? Default: FALSE |
if returnValue == 'all', a list, else a named numeric vector. If a named numeric vector, names are gene names (row names) and values are fold changes if returnValue == 'fc' or p values of returnValue == 'p'. The number of genes returned depends on whether returnAllGenes == T and whether cutoff.fc and cutoff.p were given (default is that they are).