annotate: Annotation based on GO terms

In DISC-IISR/RNAseqAnalysis: A List of Relevent Functions RNA-seq data analysis

Description

Provides user with GO annotation and graphs for all the three GO terms i.e., Molecular Function, Biological Process and Cellular Components

Usage

annotate(filter = c(Fold = 2, FDR = 10), id_type = "gene", CLSZ = 2,
  cutoff = 0.01)

Arguments

filter	Named vector with filter cutoffs of format c(Fold=2, FDR=10) where Fold refers to the fold change cutoff (unlogged) and FDR to the p-value cutoff, default value is Fold=2, FDR=10.
id_type	specifies type of IDs in input, can be assigned gene or affy, default is gene.
CLSZ	minimum gene set (cluster) size to consider. Gene sets below this cutoff will be ignored, default value is 2.
cutoff	p-value cutoff for GO terms to show in result data.frame, default is 0.01.

See Also

useMart

Examples

## Not run: 
annotate()
annotate(filter=c(Fold=2, FDR=70), id_type="gene", CLSZ=2, cutoff=0.01)

## End(Not run)

DISC-IISR/RNAseqAnalysis documentation built on May 9, 2019, 8:10 a.m.