goana: Gene Ontology or KEGG Analysis of Differentially Expressed...

In hiraksarkar/edgeR_fork: Empirical Analysis of Digital Gene Expression Data in R

Description

Test for over-representation of gene ontology (GO) terms or KEGG pathways in the up and down differentially expressed genes from a linear model fit.

Usage

## S3 method for class 'DGELRT'
goana(de, geneid = rownames(de), FDR = 0.05, trend = FALSE, ...)
## S3 method for class 'DGELRT'
kegga(de, geneid = rownames(de), FDR = 0.05, trend = FALSE, ...)

Arguments

de	an DGELRT or DGEExact object.
geneid	gene IDs. Either a character vector of length nrow(de) or the name of the column of de$genes containing the Gene IDs.
FDR	false discovery rate cutoff for differentially expressed genes. Numeric value between 0 and 1.
trend	adjust analysis for gene length or abundance? Can be logical, or a numeric vector of covariate values, or the name of the column of de$genes containing the covariate values. If TRUE, then de$AveLogCPM is used as the covariate.
...	any other arguments are passed to goana.default or kegga.default.

Details

goana performs Gene Ontology enrichment analyses for the up and down differentially expressed genes from a linear model analysis. kegga performs the corresponding analysis for KEGG pathways.

The argument de should be a fitted model object created by glmLRT, glmTreat, glmQLFTest or exactTest.

For goana, the gene IDs must be Entrez Gene IDs. These can be supplied either as row.names of de or as a column of de$genes. In the latter case, the column name containing the Entrez IDs is given by geneid. Alternatively, if the Entrez IDs are not part of the de object, then they can be supplied as a vector argument to geneid.

For kegga, gene IDs other than Entrez Gene IDs are supported for some species. See kegga.default for more information.

If trend=FALSE, the function computes one-sided hypergeometric tests equivalent to Fisher's exact test.

If trend=TRUE or a covariate is supplied, then a trend is fitted to the differential expression results and the method of Young et al (2010) is used to adjust for this trend. The adjusted test uses Wallenius' noncentral hypergeometric distribution.

Value

goana produces a data.frame with a row for each GO term and the following columns:

Term	GO term.
Ont	ontology that the GO term belongs to. Possible values are "BP", "CC" and "MF".
N	Number of genes in the GO term.
Up	number of up-regulated differentially expressed genes.
Down	number of down-regulated differentially expressed genes.
P.Up	p-value for over-representation of GO term in up-regulated genes.
P.Down	p-value for over-representation of GO term in down-regulated genes.

The row names of the data frame give the GO term IDs.

kegga produces a data.frame as above except that the rownames are KEGG pathway IDs, Term become Path and there is no Ont column.

Author(s)

Yunshun Chen and Gordon Smyth

References

Chen Y, Lun ATL, and Smyth, GK (2016). From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline. F1000Research 5, 1438. https://f1000research.com/articles/5-1438

Young, M. D., Wakefield, M. J., Smyth, G. K., Oshlack, A. (2010). Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biology 11, R14. http://genomebiology.com/2010/11/2/R14

See Also

goana, topGO, kegga, topKEGG

Examples

## Not run: 
fit <- glmFit(y, design)
lrt <- glmLRT(fit)
go <- goana(lrt, species="Hs")
topGO(go, ont="BP", sort="up")
topGO(go, ont="BP", sort="down")
## End(Not run)

hiraksarkar/edgeR_fork documentation built on Dec. 20, 2021, 3:52 p.m.