DEG rdata annotation assumes human reference

[epartan]

DEG template, load_counts_data chunk to create rdata object from AnnotationDbi

rdata = AnnotationDbi::select(org.Hs.eg.db, rownames(counts), 'SYMBOL', 'ENSEMBL') %>% dplyr::select(gene_id = ENSEMBL, gene_name = SYMBOL)
Assumes human reference

Should base reference used off of genome set in parameters at top of file

If using mouse reference, need the following:

1. In libraries:
   # BiocManager::install("org.Mm.eg.db")
library(org.Mm.eg.db)

2. In load_counts_data chunk to create rdata object
   rdata = AnnotationDbi::select(org.Mm.eg.db, rownames(counts), 'SYMBOL', 'ENSEMBL') %>% dplyr::select(gene_id = ENSEMBL, gene_name = SYMBOL)

[epartan]

This is also true in the Pathway Enrichment section at the end of the DEG template.

Need to change org.Hs.eg.db > org.Mm.eg.db and "human" to "Mus musculus"

universe=res %>% filter(!is.na(padj)) %>% pull(gene_id)
mapping = AnnotationDbi::select(org.Mm.eg.db, universe, 'ENTREZID', 'ENSEMBL')

all_in_life=list(
msigdbr(species = "Mus musculus", category = "H") %>% mutate(gs_subcat="Hallmark"),
msigdbr(species = "Mus musculus", category = "C2", subcategory = "CP:REACTOME"),
msigdbr(species = "Mus musculus", category = "C2", subcategory = "CP:KEGG"),
msigdbr(species = "Mus musculus", category = "C2", subcategory = "CP:PID"),
msigdbr(species = "Mus musculus", category = "C5", subcategory = "GO:BP"),
msigdbr(species = "Mus musculus", category = "C5", subcategory = "GO:MF"),
msigdbr(species = "Mus musculus", category = "C5", subcategory = "HPO"),
msigdbr(species = "Mus musculus", category = "C3", subcategory = "TFT:GTRD"),
msigdbr(species = "Mus musculus", category = "C6") %>% mutate(gs_subcat="Oncogenic")
)

ora_input = res %>% filter(!is.na(padj), padj<0.01, abs(lfc)>0.3) %>% pull(gene_id)
input_entrezid <- AnnotationDbi::select(org.Mm.eg.db, ora_input, 'ENSEMBL', columns = c('ENTREZID', 'SYMBOL'))