inst/hgncLookup.R

In lwaldron/MistakenIdentities: Handy Functions for Working With HGNC Gene Symbols and Affymetrix Probeset Identifiers.

map <- read.delim("http://www.genenames.org/cgi-bin/hgnc_downloads?col=gd_hgnc_id&col=gd_app_sym&col=gd_prev_sym&col=gd_aliases&status=Approved&status=Entry+Withdrawn&status_opt=2&where=&order_by=gd_hgnc_id&format=text&limit=&hgnc_dbtag=on&submit=submit", as.is=TRUE)

if(file.exists("extdata/"))
    save(map, file="extdata/genenames_org.rda", compress="bzip2")

M  <- do.call(rbind, apply(map[nchar(map[, 3])>0 | nchar(map[, 4])>0 , ], 1,
function(x) {
    y <- strsplit(paste(x[3:4], collapse=", "), ", ")[[1]]
    cbind(y[y!=""], x[2])
    }))
N <- map[nchar(map[, 3])==0, c(2, 2)]
id <- grep("withdrawn", N[, 1])
N[id, 2] <- NA
N[, 1] <- gsub("~withdrawn", "", N[, 1])

O = read.csv(system.file("extdata/mog_map.csv", package = "HGNChelper"),
             as.is=TRUE)[, 2:1]
O$mogrified <- toupper(O$mogrified)

colnames(M) <- c("Symbol", "Approved.Symbol")
colnames(N) <- c("Symbol", "Approved.Symbol")
colnames(O) <- c("Symbol", "Approved.Symbol")

hgnc.table <- rbind(M, N, O)

## remove withdrawn symbols with known new name
hgnc.table <- hgnc.table[!(duplicated(hgnc.table$Symbol) & is.na(hgnc.table$Approved.Symbol)), ]
hgnc.table <- hgnc.table[order(hgnc.table$Symbol), ]

hgnc.table$Symbol <- as.character(hgnc.table$Symbol)
hgnc.table$Approved.Symbol <- as.character(hgnc.table$Approved.Symbol)
rownames(hgnc.table) <- 1:nrow(hgnc.table)

## In the un-approved column, convert everything but orfs to upper-case:
hgnc.table$Symbol <- toupper(hgnc.table$Symbol)
hgnc.table$Symbol <- sub("(.*C[0-9XY]+)ORF(.+)", "\\1orf\\2", hgnc.table$Symbol)

hgnc.table <- unique(hgnc.table)

if(file.exists("../data/"))
    save(hgnc.table, file="../data/hgnc.table.rda", compress="bzip2")