Add hgnc symbol to expression set.

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Description

Function first maps entrez gene ids to homologous human entrez gene ids and then to hgnc symbols.

Usage

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symbol_annot(eset, gse_name = "")

Arguments

eset

Expression set to annotate.

gse_name

GSE name for eset.

Details

Initial entrez gene ids are obtained from bioconductor annotation data packages or from feature data of supplied expression set. Homologous human entrez ids are obtained from homologene and then mapped to hgnc symbols using org.Hs.eg.db. Expression set is expanded if 1:many mappings occur.

Value

Expression set with hgnc symbols ("SYMBOL") and row names ("PROBE") added to fData slot.

See Also

load_raw.

Examples

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library(lydata)

# location of raw data
data_dir <- system.file("extdata", package = "lydata")

# load eset
eset <- load_raw("GSE9601", data_dir)[[1]]

# annotate eset (need if load_raw failed to annotate)
eset <- symbol_annot(eset)