dropECode: Drop GO labels for specified Evidence Codes
In annotate: Annotation for microarrays
Description
Usage
Arguments
Details
Value
Author(s)
See Also
Examples
Description
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.
Usage
1
dropECode(inlist, code="IEA")
Arguments
inlist
A list of GO data
code
The set of codes that should be dropped.
Details
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.
Value
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.
Author(s)
R. Gentleman
See Also
Examples
1
2
3
4
5
6
library("hgu95av2.db")
bb <- hgu95av2GO[["39613_at"]]
getEvidence(bb[1:3])
cc <- dropECode(bb[1:3])
if (length(cc))
getEvidence(cc)
annotate documentation built on Nov. 8, 2020, 8:14 p.m.
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Description Usage Arguments Details Value Author(s) See Also Examples
Description
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.
Usage
1 | dropECode(inlist, code="IEA")
|
Arguments
inlist |
A list of GO data |
code |
The set of codes that should be dropped. |
Details
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.
Value
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.
Author(s)
R. Gentleman
See Also
Examples
1 2 3 4 5 6 | library("hgu95av2.db")
bb <- hgu95av2GO[["39613_at"]]
getEvidence(bb[1:3])
cc <- dropECode(bb[1:3])
if (length(cc))
getEvidence(cc)
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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