c5.go.mapping: MSigDB C5 GO term to GO ID mapping

In RamiGO: AmiGO visualize R interface

Description

This object provides a mapping for MSigDB GO terms for the bp, mf and cc GO categories to official GO ID's.

Format

A data frame with 1454 observations on the following 2 variables.

description

a character vector of MSigDB GO terms

goid

a character vector of official GO ID's

Source

c5.go.mapping:

http://www.broadinstitute.org/gsea/msigdb/collections.jsp#C5

References

Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP. Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences of the United States of America 2005 Oct;102(43):15545 -15550.

Examples

## load the mapping
data(c5.go.mapping)

## look at the object
str(c5.go.mapping)

## create go term vector
terms <- c("CHROMATIN_REMODELING_COMPLEX",
	"RNA_POLYMERASE_COMPLEX",
	"CYTOKINESIS","CELL_RECOGNITION")
id <- sapply(terms,function(x)c5.go.mapping[
  match(x,c5.go.mapping[,1]),2])
id

Example output

Loading required package: gsubfn
Loading required package: proto
Warning message:
no DISPLAY variable so Tk is not available 
'data.frame':	1454 obs. of  2 variables:
 $ description: chr  "NUCLEOPLASM" "EXTRINSIC_TO_PLASMA_MEMBRANE" "ORGANELLE_PART" "CELL_PROJECTION_PART" ...
 $ goid       : chr  "GO:0005654" "GO:0019897" "GO:0044422" "GO:0044463" ...
CHROMATIN_REMODELING_COMPLEX       RNA_POLYMERASE_COMPLEX 
                "GO:0016585"                 "GO:0030880" 
                 CYTOKINESIS             CELL_RECOGNITION 
                "GO:0000910"                 "GO:0008037" 

RamiGO documentation built on May 2, 2018, 3:30 a.m.