agGO2PROBE {ag} | R Documentation |
agGO2PROBE is an R environment that provides mappings between GO identifiers and manufacturer identifiers.
Each GO term maps to a named vector of manufacturer identifiers. The name associated with each manufacturer identifier corresponds to the evidence code for that GO identifier. The evidence code indicates what kind of evidence supports the association between the GO and Entrez Gene identifiers. Evidence codes currently in use include:
IMP - inferred from mutant phenotype
IGI - inferred from genetic interaction
IPI - inferred from physical interaction
ISS - inferred from sequence similarity
IDA - inferred from direct assay
IEP - inferred from expression pattern
IEA - inferred from electronic annotation
TAS - traceable author statement
NAS - non-traceable author statement
ND - no biological data available
IC - inferred by curator
A GO identifier may be mapped to the same probe identifier more than once but the evidence code can be different. Mappings between Gene Ontology identifiers an Gene Ontology terms and other information are available in a separate data package named GO.
Mappings were based on data provided by:
Entrez Gene Tair: ftp://ftp.arabidopsis.org/home/tair/Microarrays/Affymetrix/affy_AG_array_elements-2006-07-14.txt Tair: ftp://ftp.arabidopsis.org/home/tair/Genes/TAIR_sequenced_genes Tair: ftp://ftp.arabidopsis.org/home/tair/User_Requests/LocusPublished.02022007 Built: N/A.
Package built Fri Aug 24 17:42:16 2007
ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/
# Convert to a list xx <- as.list(agGO2PROBE) if(length(xx) > 0){ # Gets the probe identifiers for the top 2nd and 3nd GO identifiers goids <- xx[2:3] # Gets the probe identifiers for the first element of goids goids[[1]] # Evidence code for the mappings names(goids[[1]]) }