GeneTonicList: Create a GeneTonicList object

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

Create a GeneTonicList object

Description

Create a list for GeneTonic from the single required components.

Usage

GeneTonicList(dds, res_de, res_enrich, annotation_obj)

GeneTonic_list(dds, res_de, res_enrich, annotation_obj)

Arguments

dds	A DESeqDataSet object, normally obtained after running your data through the DESeq2 framework.
res_de	A DESeqResults object. As for the dds parameter, this is also commonly used in the DESeq2 framework.
res_enrich	A data.frame object, storing the result of the functional enrichment analysis. Required columns for enjoying the full functionality of GeneTonic() include: a gene set identifier (e.g. GeneOntology id, gs_id) and its term description (gs_description) a numeric value for the significance of the enrichment (gs_pvalue) a column named gs_genes containing a comma separated vector of the gene names associated to the term, one for each term the number of genes in the geneset of interest detected as differentially expressed (gs_de_count), or in the background set of genes (gs_bg_count) See shake_topGOtableResult() or shake_enrichResult() for examples of such formatting helpers
annotation_obj	A data.frame object, containing two columns, gene_id with a set of unambiguous identifiers (e.g. ENSEMBL ids) and gene_name, containing e.g. HGNC-based gene symbols. This object can be constructed via the org.eg.XX.db packages, e.g. with convenience functions such as mosdef::get_annotation_orgdb().

Details

Having this dedicated function saves the pain of remembering which names the components of the list should have. For backwards compatibility, the GeneTonic_list function is still provided as a synonim, and will likely be deprecated in the upcoming release cycles.

Value

A GeneTonic-list object, containing in its named slots the arguments specified above: dds, res_de, res_enrich, and annotation_obj - the names of the list are specified following the requirements for using it as single input to GeneTonic()

Author(s)

Federico Marini

Examples

library("macrophage")
library("DESeq2")
library("org.Hs.eg.db")
library("AnnotationDbi")

# dds object
data("gse", package = "macrophage")
dds_macrophage <- DESeqDataSet(gse, design = ~ line + condition)
rownames(dds_macrophage) <- substr(rownames(dds_macrophage), 1, 15)
dds_macrophage <- estimateSizeFactors(dds_macrophage)

# annotation object
anno_df <- data.frame(
  gene_id = rownames(dds_macrophage),
  gene_name = mapIds(org.Hs.eg.db,
    keys = rownames(dds_macrophage),
    column = "SYMBOL",
    keytype = "ENSEMBL"
  ),
  stringsAsFactors = FALSE,
  row.names = rownames(dds_macrophage)
)


# res object
data(res_de_macrophage, package = "GeneTonic")
res_de <- res_macrophage_IFNg_vs_naive

# res_enrich object
data(res_enrich_macrophage, package = "GeneTonic")
res_enrich <- shake_topGOtableResult(topgoDE_macrophage_IFNg_vs_naive)
res_enrich <- get_aggrscores(res_enrich, res_de, anno_df)

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

# now everything is in place to launch the app
if (interactive()) {
  GeneTonic(gtl = gtl_macrophage)
}

federicomarini/GeneTonic documentation built on Dec. 21, 2024, 10:05 p.m.