Description Usage Arguments Details Value Author(s) References See Also Examples
Functionality to map between common gene ID types such as ENSEMBL and ENTREZ for gene expression datasets, gene sets, and gene regulatory networks.
1 2 3 4 5 6 7 8 9 10 |
obj |
The object for which gene IDs should be mapped. Supported options include
|
org |
Character. Organism in KEGG three letter code, e.g. ‘hsa’ for ‘Homo sapiens’. See references. |
from |
Character. Gene ID type from which should be mapped. Corresponds
to the gene ID type of argument |
to |
Character. Gene ID type to which should be mapped. Corresponds to
the gene ID type the argument |
multi.to |
How to resolve 1:many mappings, i.e. multiple to.IDs for a
single from.ID? This is passed on to the |
multi.from |
How to resolve many:1 mappings, i.e. multiple from.IDs
mapping to the same to.ID? Only applicable if
Note that a user-defined function can also be supplied for custom behaviors.
This will be applied for each case where there are multiple from.IDs for a
single to.ID, and accordingly takes the arguments |
The function 'idTypes' lists the valid values which the arguments 'from' and 'to' can take. This corresponds to the names of the available gene ID types for the mapping.
idTypes: character vector listing the available gene ID types for the mapping;
idMap: An object of the same class as the input argument obj
, i.e.
a SummarizedExperiment
if provided an expression dataset,
a list of character vectors or a GeneSetCollection
if
provided gene sets, and a character matrix if provided a gene regulatory network.
Ludwig Geistlinger <Ludwig.Geistlinger@sph.cuny.edu>
KEGG Organism code http://www.genome.jp/kegg/catalog/org_list.html
SummarizedExperiment
, mapIds
,
keytypes
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 | # (1) ID mapping for gene expression datasets
# create an expression dataset with 3 genes and 3 samples
se <- makeExampleData("SE", nfeat = 3, nsmpl = 3)
names(se) <- paste0("ENSG00000000", c("003", "005", "419"))
idMap(se, org = "hsa")
# user-defined mapping
rowData(se)$MYID <- c("g1", "g1", "g2")
idMap(se, to = "MYID")
# data-driven resolving of many:1 mappings
## e.g. select from.ID with lowest p-value
pcol <- configEBrowser("PVAL.COL")
rowData(se)[[pcol]] <- c(0.001, 0.32, 0.15)
idMap(se, to = "MYID", multi.from = "minp")
## ... or using a customized function
maxScore <- function(ids, se)
{
scores <- rowData(se)[ids, "SCORE"]
ind <- which.max(scores)
return(ids[ind])
}
rowData(se)$SCORE <- c(125.7, 33.4, 58.6)
idMap(se, to = "MYID", multi.from = maxScore)
# (2) ID mapping for gene sets
# create two gene sets containing 3 genes each
s2 <- paste0("ENSG00000", c("012048", "139618", "141510"))
gs <- list(s1 = names(se), s2 = s2)
idMap(gs, org = "hsa", from = "ENSEMBL", to = "SYMBOL")
# (3) ID mapping for gene regulatory networks
grn <- cbind(FROM = gs$s1, TO = gs$s2, TYPE = rep("+", 3))
idMap(grn, org = "hsa", from = "ENSEMBL", to = "ENTREZID")
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