inst/extdata/help_gtl.md

In federicomarini/GeneTonic: Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional Enrichment Analysis

GeneTonic requires you to provide as input a GeneTonicList, i.e. a list-like object, storing four essential components, based on the widely used DESeq2 framework. If you are using alternative workflows, you might need to convert them beforehand. A GeneTonicList contains these named slots:

1. dds, a DESeqDataSet object storing all the information related to the expression matrix.
2. res_de, the DESeqResults object with the results of Differential Expression analysis.
3. res_enrich, a simple data frame with the results from functional enrichment analysis tools (see the documentation to find out which tools are supported via the shaker_* functions). Column names must follow some specific requirements to guarantee interoperability within GeneTonic.
4. annotation_obj, the annotation data frame, composed at least of two columns, gene_id, with a set of unambiguous identifiers (e.g. ENSEMBL ids) corresponding to the row names of the dds object, and gene_name, containing e.g. HGNC-based gene symbols.

You can create a GeneTonicList by calling

mygtlobject <- GeneTonicList(
  dds = dds,
  res_de = res_de,
  res_enrich = res_enrich,
  annotation_obj = anno_df
)

If desired, you can export the GeneTonicList to a serialized object, and then upload this in the current panel of the GeneTonic app:

saveRDS(mygtlobject, file = "mygtlobject.RDS")

If running GeneTonic from the command line, you can simply execute these lines to run a full example on the macrophage dataset:

library("GeneTonic")
example("GeneTonic", ask = FALSE)

For additional information about the format, you can refer to

• the GeneTonic package vignette (to be found at http://bioconductor.org/packages/GeneTonic/)
• the original GeneTonic publication (https://doi.org/10.1186/s12859-021-04461-5, on BMC Bioinformatics), in particular the workflow depicted in Figure 1
• a series of protocols to appear in Current Protocols in Bioinformatics, where GeneTonic is featured, together with the pcaExplorer and ideal packages

federicomarini/GeneTonic documentation built on Oct. 10, 2024, 8:49 p.m.