convertId: convertId

In slzhao/KEGGprofile: An annotation and visualization package for multi-types and multi-groups expression data in KEGG pathway

Description

A function to convert ID based on the biomaRt package.

Usage

convertId(x, dataset = "hsapiens_gene_ensembl",
  filters = "uniprotswissprot", attributes = c(filters,
  "entrezgene_id"), genesKept = c("foldchange", "first", "random", "var",
  "abs"), keepNoId = T, keepMultipleId = F, verbose = F)

Arguments

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.

Details

A function to convert ID based on the biomaRt package..

Examples

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_id",attributes =c("entrezgene_id","uniprotswissprot"),
keepNoId=FALSE)

## End(Not run)

slzhao/KEGGprofile documentation built on Oct. 27, 2020, 4:29 a.m.