Friday, April 11, 2014

Mapping between Affymetrix exon array Features to Genes

library(biomaRt)
mart.hs <- useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl")
# get probeset IDs for transcript cluster 2315633
huex <- read.table("~/Downloads/HuEx-1_0-st-v2.na32.hg19.probeset.csv", sep = ",", stringsAsFactors = F, header = T)
probes <- subset(huex, transcript_cluster_id == "2315633")$probeset_id
# get gene symbols
genes <- getBM(attributes = c("affy_huex_1_0_st_v2", "hgnc_symbol"), filters = "affy_huex_1_0_st_v2", values = probes, mart = mart.hs)
genes
#  affy_huex_1_0_st_v2 hgnc_symbol
#1             2315638     B3GALT6
#2             2315642     B3GALT6
#3             2315639     B3GALT6
#4             2315643     B3GALT6
#5             2315644     B3GALT6
#6             2315640     B3GALT6
#7             2315637     B3GALT6
#8             2315645     B3GALT6
#9             2315641     B3GALT6

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