checkup_gtl: Checking the 'gtl' input object for GeneTonic

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

Checking the gtl input object for GeneTonic

Description

Checking the gtl ("GeneTonic list") input object for GeneTonic, with the correct content and format expected

Usage

checkup_gtl(gtl, verbose = FALSE)

Arguments

gtl

A DESeqDataSet object, normally obtained after running your data through the DESeq2 framework. This list should contain in the dds slot: A DESeqDataSet object in the res_de: A DESeqResults object in the res_enrich: A data.frame object, storing the result of the functional enrichment analysis in the 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.

verbose

Logical, to control level of verbosity of the messages generated

Details

Some suggestions on the requirements for the gtl are returned in the error messages.

Value

Invisible NULL

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

checkup_gtl(gtl)
# if all is fine, it should return an invisible NULL and a simple message

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