mt_diffexprs: Calculate differential expression statistics by a grouping...
In TYMichaelsen/mmtravis: Tools for analysing (meta)transcriptomics data

Description Usage Arguments Details Value Author(s) Examples

mt_diffexprs

1	mt_diffexprs(obj,group)

`obj`	(required) An object of class 'mmt' (see `mt_load`) or 'ampvis2' (see `amp_load`).
`group`	(required) Character string defining the grouping variable to use for differential expression.
`Genome`	(optional) If provided, character string defining the grouping variable in `mt$mtgene` to perform genome-specific normalization (See details).
`intercept`	(optional) Specify the level of 'group' to be used as reference/intercept. Default is by alphabetical order.
`row_labels`	(optional) Specify columns of rowdata to print on heatmap.
`order_var_by`	(optional) How to order rows of heatmap. You can specify 1) "variance" or 2) one of the levels in `group`, which will order according to the absolute value of that level. (default: "variance")
`row_show`	(optional) The number of rows to show.

Typically one would subset low-expression genes (use mt_subset) before performing the analysis, due to a low signal/noise ratio. This also drastically reduces computation times and improves stability of the parameter estimation. If the parameter Genome is set, a genome-specific normalization of the count matrix is performed prior to standard DESeq2 analysis. For more details see Klingenberg & Meinicke (2017).

A list with 2 elements:

heatmap - A heatmap showing the log fold-change of each level in group relative to the intercept/baseline level specified in intercept. The intercept is therefore not possible to plot.
DESeq - A DESeqDataSet containing the results of the differential expression analysis. To extract results and do comparisons between groups use the mt_dumpDE function.

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,nom = "ELECTRODE",denom = "SUSPENTION")

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

## End(Not run)