#' Change the GENOMEacc from gene2refseq into a chromosome name
#'
#' Currently supports mouse, human and rat. For new organisms, find
#' out the chromosome accession numbers by searching for them in the
#' tmp genome page:
#' eg: try searching for "rattus AND norvegicus AND chromosome" in
#' http://www.tmp.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=genome
#'
#' @author Mark Cowley, 14 April 2006
#' @export
accession2chr <- function(x, taxid=10090) {
if( taxid == TAXID.MOUSE ) {
chr <- c( "NC_000067", # chr 1
"NC_000068", # chr 2
"NC_000069", # chr 3
"NC_000070", # chr 4
"NC_000071", # chr 5
"NC_000072", # chr 6
"NC_000073", # chr 7
"NC_000074", # chr 8
"NC_000075", # chr 9
"NC_000076", # chr 10
"NC_000077", # chr 11
"NC_000078", # chr 12
"NC_000079", # chr 13
"NC_000080", # chr 14
"NC_000081", # chr 15
"NC_000082", # chr 16
"NC_000083", # chr 17
"NC_000084", # chr 18
"NC_000085", # chr 19
"NC_000086", # chr X
"NC_000087", # chr Y
"NC_005089") # Mitochondrion
names(chr) <- c(as.character(1:19), "X", "Y", "M")
}
else if( taxid == TAXID.HUMAN ) {
# http://www.ncbi.nlm.nih.gov/genome/guide/human/release_notes.html
chr <- c( "NC_000001", # chr 1
"NC_000002", # chr 2
"NC_000003", # chr 3
"NC_000004", # chr 4
"NC_000005", # chr 5
"NC_000006", # chr 6
"NC_000007", # chr 7
"NC_000008", # chr 8
"NC_000009", # chr 9
"NC_000010", # chr 10
"NC_000011", # chr 11
"NC_000012", # chr 12
"NC_000013", # chr 13
"NC_000014", # chr 14
"NC_000015", # chr 15
"NC_000016", # chr 16
"NC_000017", # chr 17
"NC_000018", # chr 18
"NC_000019", # chr 19
"NC_000020", # chr 20
"NC_000021", # chr 21
"NC_000022", # chr 22
"NC_000023", # chr X
"NC_000024", # chr Y
"NC_001807") # Mitochondrion
names(chr) <- c(as.character(1:22), "X", "Y", "M")
}
else if( taxid == TAXID.RAT ) {
chr <- c("NC_005100", # chr 1
"NC_005101", # chr 2
"NC_005102", # chr 3
"NC_005103", # chr 4
"NC_005104", # chr 5
"NC_005105", # chr 6
"NC_005106", # chr 7
"NC_005107", # chr 8
"NC_005108", # chr 9
"NC_005109", # chr 10
"NC_005110", # chr 11
"NC_005111", # chr 12
"NC_005112", # chr 13
"NC_005113", # chr 14
"NC_005114", # chr 15
"NC_005115", # chr 16
"NC_005116", # chr 17
"NC_005117", # chr 18
"NC_005118", # chr 19
"NC_005119", # chr 20
"NC_005120") # chr X
names(chr) <- c(as.character(1:20), "X")
}
else {
stop( "unsupported taxon. see function description for adding new taxa." )
}
res <- rep(NA, length(x))
for(i in 1:length(chr)) {
## res[grep(paste0(chr[i], "\\."), x)] <- names(chr)[i]
res[grep(chr[i], x)] <- names(chr)[i]
}
return( res )
}
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