Checking the input objects for GeneTonic — checkup

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

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

Value

Invisible NULL

Details

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

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)
#> using counts and average transcript lengths from tximeta
rownames(dds_macrophage) <- substr(rownames(dds_macrophage), 1, 15)
dds_macrophage <- estimateSizeFactors(dds_macrophage)
#> using 'avgTxLength' from assays(dds), correcting for library size

# 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)
)
#> 'select()' returned 1:many mapping between keys and columns

# 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)
#> Found 500 gene sets in `topGOtableResult` object.
#> Converting for usage in GeneTonic...
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