Description Usage Arguments Details Value Author(s) References See Also Examples
Takse as input gene IDs in a convention, say REFSEQ, and converts them to another convention.
1 2 3 | gene.mapping(ids, inputType = "REFSEQ", outputType = "SYMBOL",
leaveNA = TRUE, inputDb = "Human", outputDb = inputDb,
verbose = 0)
|
ids |
A character vector of input gene IDs |
inputType |
The type of input IDs. |
outputType |
The type of output IDs. If it is a character vector, mapping will be done for each element. |
leaveNA |
If |
inputDb |
The input data base. Use |
outputDb |
The output data base. If it is a list, mapping will be done for each element. |
verbose |
The integer level of verbosity. 0 means silent and higher values produce more details of computation. |
It can map homologous genes between species e.g. from mouse to human. If more than 1 ID found for an input gene, only one of them is returned.
A matrix of characters with 3 columns: input, output1, and
output2. The last one is guaranteed not to be NA
.
Amir Foroushani, Habil Zare, and Rupesh Agrahari
Pages H, Carlson M, Falcon S and Li N. AnnotationDbi: Annotation Database Interface. R package version 1.32.3.
AnnotationDb-class
,
org.Hs.eg.db
org.Mm.eg.db
1 2 3 4 5 6 7 8 9 10 11 | library(org.Hs.eg.db)
g1 <- gene.mapping(ids="NM_001159995")
print(g1)
## Mapping to multiple convention
library(org.Mm.eg.db)
g2 <- gene.mapping(ids=c("NM_170730", "NM_001013580"),
inputType="REFSEQ", inputDb=org.Mm.eg.db,
outputType=c("SYMBOL","ENTREZID"),
outputDb=list(org.Hs.eg.db,org.Mm.eg.db), verbose=1)
print(g2)
|
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