mt_dumpDE: Extract results from DE analysis done using 'mt_diffexprs'.
In TYMichaelsen/mmtravis: Tools for analysing (meta)transcriptomics data

Description Usage Arguments Value Author(s) Examples

mt_dumpDE

1	mt_dumpDE(mmtDE,num,denom)

`mmtDE`	(required) An object of class `mmtDE`. See `mt_diffexprs`.
`num`	(required) Level that should be in the numerator when doing the DE analysis.
`denom`	(required) Level that should be in the denominator (i.e. the reference) when doing the DE analysis. If set to "rest", the DE analysis is done as a one-vs-all test. See XXX for details.
`sub_genes`	The genes to include in the MA and boxplot. default: all genes)
`signif`	The threshold for adjusted p-value to be considered significant. (default: 0.01)
`text_MAplot_size`	Size of text on the MA plot. (default: 3)
`ngenes_show`	The number of genes to show in the boxplot. (default: 10)
`order_by`	Order the boxplot and table by a statistic from the DE analysis. One of: (default: "logFC")
`table_full`	(logical) Output entire results table without filtering by significance. (default: FALSE)
`annot_size`	The size of text in the MA plot. (default: 5) logFC - the absolute log2 fold-change betweem `num` and `denom`. padj - the adjusted p-value of the DE analysis.
`...`	Additional arguments parsed to the `vis_boxplot` function.

A list with 3 elements:

MAplot - A MAplot (ggplot-object) with the gene expression plotted against the log2 fold-change.
BOXplot - A faceted boxplot showing the expression of the most interesting genes, grouped according to the DE analysis design.
Table - A table with the variable metadata and associated statistics from the DE analysis.

Thomas Yssing Michaelsen tym@bio.aau.dk

## Not run: 
# Load data.
data("example_mmt")

# Compute the statistics.
DE_mt <- mt_diffexprs(example_mmt,
  group      = "Type",
  row_labels = c("GeneID","product"),
  intercept  = "ANAMMOX")

# Extract results for given levels.
mt_res <- mt_dumpDE(DE_mt,num = "ELECTRODE",denom = "SUSPENTION")

# Show the output.
mt_res$MAplot
mt_res$BOXplot
head(mt_res$Table)

## End(Not run)