Description Usage Arguments Value Author(s) Examples
View source: R/additionalFunctions.R
This function allows to annotate different ID types using Bioconductor annotation packages (i.e. Homo.sapiens, Mus.musculus, org.Hs.eg.db, org.MeSH.Spo.972h.db, org.Mm.eg.db ...).
1 2 | AnnotateDECO(ids, id.type, attributes = NA, pack.db = "Homo.sapiens",
rm.redundant = TRUE, verbose = FALSE)
|
ids |
a character vector including IDs to annotate. |
id.type |
a character indicating what type of ID we are managing. It should match with correct ID types including in annotation package ("Homo.sapiens" by default). |
attributes |
a character indicating which types of ID should annotate the original IDs. It should match with correct ID types including in annotation package (Homo.sapiens by default). |
pack.db |
name of the Bioconductor annotation package to use. |
rm.redundant |
logical indicating if redundant annotation (i.e. two different HGNC symbols for the same EntrezID) should be removed or not. |
verbose |
logical indicating if messages should be displayed. |
This function returns a data.frame
containing original IDs and corresponding attributes to each one.
Francisco Jose Campos Laborie <fjcamlab@usal.es>
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | ##### Annotation example
# Select an appropiate 'id.type' depending on which annotation
# package will be used.
# library(Homo.sapiens)
# columns(Homo.sapiens)
# Selecting first 10 original IDs from ALCL dataset
data(ALCLdata)
ids <- rownames(assay(ALCL))[1:10]
## Not run as example
# annot <- AnnotateDECO(ids, id.type = "ENSEMBL",
# attributes = c("SYMBOL","CHR","GENENAME"),
# pack.db = "Homo.sapiens", rm.redundant = TRUE)
|
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