checkup_GeneTonic: Checking the input objects for GeneTonic

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

Checking the input objects for GeneTonic

Description

Checking the input objects for GeneTonic, whether these are all set for running the app

Usage

checkup_GeneTonic(dds, res_de, res_enrich, annotation_obj, verbose = FALSE)

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. See more in the main function, GeneTonic(), to check the formatting requirements (a minimal set of columns should be present).
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 each parameter 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)

checkup_GeneTonic(
  dds = dds_macrophage,
  res_de = res_de,
  res_enrich = res_enrich,
  annotation_obj = anno_df
)
# 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.