AnnotateDECO: DECO annotating function

In fjcamlab/deco: Decomposing Heterogeneous Cohorts using Omic Data Profiling

Description

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 ...).

Usage

AnnotateDECO(ids, id.type, attributes = NA, pack.db = "Homo.sapiens",
                      rm.redundant = TRUE, verbose = FALSE)

Arguments

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.

Value

This function returns a data.frame containing original IDs and corresponding attributes to each one.

Author(s)

Francisco Jose Campos Laborie <[e-mail]>

Examples

##### 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)

fjcamlab/deco documentation built on Nov. 8, 2021, 12:12 p.m.