Extract results from DE analysis done using mt_diffexprs.

mt_dumpDE

mt_dumpDE(mmtDE,num,denom)

Arguments

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.

Value

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.

Details

Examples



# 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)
# }