run_hypergeometric: Run hypergeometric test

In vari-bbc/bbcRNA: Bulk RNA-seq workflow for VAI BBC

Description

Run hypergeometric test

Usage

run_hypergeometric(x, ...)

## S4 method for signature 'data.frame'
run_hypergeometric(
  x,
  gene_set = "reactome",
  organism,
  orgDb,
  split_by_lfc_dir = TRUE,
  padj_cutoff = 0.05,
  lfc_cutoff = 0,
  ...
)

## S4 method for signature 'BbcSE'
run_hypergeometric(
  x,
  de_pkg = "edger",
  contrast_names = "",
  split_by_lfc_dir = TRUE,
  ...
)

Arguments

x	A BbcSE object.
...	Passed to enrichKEGG, enrichGO, enrichPathway or enricher. See each function for possible arguments.
gene_set	one of "kegg", "reactome", "H", "C1", "C2", "C3", "C4", "C5", "C6", "C7"
organism	For compatibility with dowstream tools, the organism is specified differently depending on the desired gene set. For KEGG, use the three-letter code according to http://www.genome.jp/kegg/catalog/org_list.html. For Reactome, possible values are ‘celegans’, ‘fly’, ‘human’, ‘mouse’, ‘rat’, ‘yeast’ and ‘zebrafish’. For msigdb, run 'msigdbr::msigdbr_show_species()'.
orgDb	OrgDB object for your organism
split_by_lfc_dir	logical. Whether DE genes should be split into up and down-regulated
padj_cutoff	numeric. Cutoff for adjusted PValue for DE.
lfc_cutoff	numeric. Cutoff for LFC (absolute value) for DE.
de_pkg	"edger" or "deseq2". Only used if x is a BbcSE
contrast_names	character value or vector for the contrast(s) of interest. See name(de_results(edger(x))). If left to default "" value then all contrasts will be processed.

Value

A list of gseaResult objects or one gseaResult object

Methods (by class)

• data.frame: x is a dataframe with gene name (entrez) as col1, log2FC as col2 and adjusted PValue as col3. Function will filter by LFC and PValue for DE genes, and optionally will split the DE genes into up and down-regulated based on LFC. The gene universe are all the genes in the dataframe. Returns a list of enrichResults for up and down-regulaed genes or just all the DE genes without regard for direction.

• BbcSE: Extract out the gene, LFC and adjusted PValue. Run run_hypergeometric for each result object (contrast).

See Also

enrichKEGG enrichGO enrichPathway enricher

vari-bbc/bbcRNA documentation built on Nov. 10, 2020, 11:09 p.m.