run_goseq: Gene ontology and pathway analysis of DE genes

In anilchalisey/parseR: Pipeline for Analysis of RNA-seq in R

Description

run_goseq is a function to perform gene ontology analysis using the goseq tool.

run_goseqmdb is a function to perform pathway analysis using the goseq tool.

Usage

run_goseq(universe = universe, degs = degs, test.cats = c("GO:BP",
  "GO:MF"), numInCat = 1000, qv = 0.05, out = ".")

run_goseqmsigdb(universe = universe, degs = degs, numInCat = 1000,
  qv = 0.05, out = "", symbol = "HGNC")

Arguments

universe	List of all genes tested for differential expression.
degs	List of differentially expressed genes.
test.cats	GO categories to test [default = c("GO:BP", "GO:MF")]
numInCat	Maximum number of genes in a GO term.
qv	Threshold q-value for significance.
out	Output directory.
symbol	Character specifying whether the gene identifiers are hgnc gene symbols ("HGNC") or entrezid ("ENTREZ").

Value

run_goseq returns a dataframe and tab-delimited file of significant GO terms.

run_goseqmsigdb returns a dataframe and tab-delimited file of significant terms from the Broad Institute's Molecular Signatures Database.

Examples

## Not run: 
universe <- unlist(as.list(rownames(counts)))
de.genes <- er$results$`OX-BUFF`$genes
gor <- run_goseq(universe, degs = de.genes)

gomdbr <- run_goseqmsigdb(universe, degs = de.genes, symbol = "HGNC")

## End(Not run)

anilchalisey/parseR documentation built on May 7, 2019, 7:45 a.m.