convertId {KEGGprofile} | R Documentation |
A function to convert ID based on the biomaRt package.
convertId(x, dataset = "hsapiens_gene_ensembl", filters = "uniprotswissprot", attributes = c(filters, "entrezgene"), genesKept = c("foldchange", "first", "random", "var", "abs"), keepNoId = T, keepMultipleId = F, verbose = F)
x |
the expression data matrix. |
dataset |
Dataset you want to use. To see the different datasets available within a biomaRt you can e.g. do: mart = useMart('ensembl'), followed by listDatasets(mart). |
filters |
Filters (one or more) that should be used in the query. A possible list of filters can be retrieved using the function listFilters. |
attributes |
Attributes you want to retrieve. A possible list of attributes can be retrieved using the function listAttributes. |
genesKept |
The method to select target gene in more than one targets. "var"/"foldchange"/"abs" means selecting the gene with largest variation/fold change/absolute value. "first" means selecting the first target and "random" means randomly selection. |
keepNoId |
Logical. Indicate keep the source IDs without target IDs or not. |
keepMultipleId |
Logical. Indicate keep the multiple target IDs related to one source ID or not. |
verbose |
Logical. Indicate report extra information on progress or not. |
A function to convert ID based on the biomaRt package..
temp<-cbind(rnorm(10),rnorm(10)) row.names(temp)<-c("Q04837","P0C0L4","P0C0L5","O75379","Q13068","A2MYD1","P60709","P30462","P30475","P30479") colnames(temp)<-c("Exp1","Exp2") convertId(temp,filters="uniprotswissprot",keepMultipleId=TRUE) ## Not run: temp<-cbind(rnorm(5000),rnorm(5000),rnorm(5000),rnorm(5000),rnorm(5000),rnorm(5000)) row.names(temp)<-1000:5999 colnames(temp)<-c("Control1","Control2","Control3","Treatment1","Treatment2","Treatment3") convertId(temp,filters="entrezgene",attributes =c("entrezgene","uniprot_swissprot"),keepNoId=FALSE) ## End(Not run)