symbol_annot: Add hgnc symbol to expression set.

In alexvpickering/crossmeta: Cross Platform Meta-Analysis of Microarray Data

Add hgnc symbol to expression set.

Description

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

Usage

symbol_annot(eset, gse_name = "", ensql = NULL)

Arguments

eset	Expression set to annotate.
gse_name	GSE name for eset.
ensql	For development. Path to sqlite file with ENTREZID and SYMBOL columns created in data-raw/entrezdt.

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

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)

alexvpickering/crossmeta documentation built on May 23, 2024, 5:06 a.m.