dropECode | R Documentation |
Genes are mapped to GO terms on the basis of evidence codes. In some analyses it will be appropriate to drop certain sets of annotations based on specific evidence codes.
dropECode(inlist, code="IEA")
inlist |
A list of GO data |
code |
The set of codes that should be dropped. |
A simple use of lapply
and sapply
to find
and eliminate those terms that have the specified evidence codes.
This might be used when one is using to GO to validate a sequence matching experiment (for example), then all terms whose mapping was based on sequence similarity (say ISS and IEA) should be removed.
A list of the same length as the input list retaining only those
annotations whose evidence codes were not the ones in the exclusion
set code
.
R. Gentleman
getEvidence
, getOntology
library("hgu95av2.db")
bb <- hgu95av2GO[["39613_at"]]
getEvidence(bb[1:3])
cc <- dropECode(bb[1:3])
if (length(cc))
getEvidence(cc)
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