Question: OFFICIAL_GENE_SYMBOL not an available idType in RDAVIDWebService
1
gravatar for chang02_23
4.6 years ago by
chang02_2320
United States
chang02_2320 wrote:

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 • 1.7k views
ADD COMMENTlink modified 4.6 years ago by James W. MacDonald51k • written 4.6 years ago by chang02_2320
Answer: OFFICIAL_GENE_SYMBOL not an available idType in RDAVIDWebService
2
gravatar for James W. MacDonald
4.6 years ago by
United States
James W. MacDonald51k wrote:

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.

 

 

ADD COMMENTlink written 4.6 years ago by James W. MacDonald51k
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