Checking the gtl input object for GeneTonic

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

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

Value

Invisible NULL

Details

Some suggestions on the requirements for the gtl 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)

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