OFFICIAL_GENE_SYMBOL not an available idType in RDAVIDWebService
1
@chang02_23-7435
Last seen 6.5 years ago
United States
I want to run a list of genes through functional annotation but I can't even upload my gene list as official_gene_symbol, which is available on the web. What are some ways to get around it?
gene=c("APC", "KRAS", "TP53")
library("RDAVIDWebService")
david<-DAVIDWebService$new("me@inst.org")
result<-addList(david, gene, idType="OFFICIAL_GENE_SYMBOL", listName="crc_gene", listType="Gene")
>Error: idType %in% getIdTypes() is not TRUE
rdavidwebservice
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@james-w-macdonald-5106
Last seen 1 day ago
United States
Convert to something that is in the IdTypes:
> gene=c("APC", "KRAS", "TP53")
> library("RDAVIDWebService")
> david<-DAVIDWebService$new("me@inst.org")
> getIdTypes(david)
[1] "AFFYMETRIX_3PRIME_IVT_ID" "AFFYMETRIX_EXON_GENE_ID"
[3] "AFFYMETRIX_SNP_ID" "AGILENT_CHIP_ID"
[5] "AGILENT_ID" "AGILENT_OLIGO_ID"
[7] "ENSEMBL_GENE_ID" "ENSEMBL_TRANSCRIPT_ID"
[9] "ENTREZ_GENE_ID" "FLYBASE_GENE_ID"
[11] "FLYBASE_TRANSCRIPT_ID" "GENBANK_ACCESSION"
[13] "GENOMIC_GI_ACCESSION" "GENPEPT_ACCESSION"
[15] "ILLUMINA_ID" "IPI_ID"
[17] "MGI_ID" "PFAM_ID"
[19] "PIR_ID" "PROTEIN_GI_ACCESSION"
[21] "REFSEQ_GENOMIC" "REFSEQ_MRNA"
[23] "REFSEQ_PROTEIN" "REFSEQ_RNA"
[25] "RGD_ID" "SGD_ID"
[27] "TAIR_ID" "UCSC_GENE_ID"
[29] "UNIGENE" "UNIPROT_ACCESSION"
[31] "UNIPROT_ID" "UNIREF100_ID"
[33] "WORMBASE_GENE_ID" "WORMPEP_ID"
[35] "ZFIN_ID"
> egids <- select(org.Hs.eg.db, gene, "ENTREZID", "SYMBOL")[,2]
> egids
[1] "324" "3845" "7157"
> result <- addList(david, egids, idType = "ENTREZ_GENE_ID", listName = "crc_gene", listType = "Gene")
> result
$inDavid
[1] 1
$unmappedIds
character(0)
I don't use RDAVIDWebServices, so I have no idea if that is a reasonable value for the result object, but that's the general idea.
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