filterTranscriptID<-function(transcript_ids,assembly,URL){
if(length(transcript_ids)!=0){
ensembl = returnEnsembl(assembly,URL)
if(!is.null(ensembl)){
data <- biomaRt::getBM(attributes = c("ensembl_gene_id","external_gene_name",
"chromosome_name", "start_position", "end_position",
"strand"),
filters = c("ensembl_transcript_id"), #listFilters(ensembl)
values = transcript_ids,
mart=ensembl,
verbose = FALSE)
names(data)<-c("geneID","geneName","chr","start","end","strand")
data <- data[c(3,4,5,6,1,2)]
if(length(data)>0){
hit<-stringr::str_detect(data$strand,"-1")
data$strand[hit]<-"-"
hit<-stringr::str_detect(data$strand,"1")
data$strand[hit]<-"+"
hit<-stringr::str_detect(data$chr,"CHR")==FALSE
data$chr[hit]<-paste("chr",data$chr[hit],sep = "")
}
return(data)
}
}else return(NULL)
}
filterTranscriptID_V<-function(transcript_ids,assembly,URL){
if(length(transcript_ids)!=0){
ensembl = returnEnsembl(assembly,URL)
if(!is.null(ensembl)){
data <- biomaRt::getBM(attributes = c("ensembl_gene_id","external_gene_name",
"chromosome_name", "start_position", "end_position",
"strand"),
filters = c("ensembl_transcript_id_version"), #listFilters(ensembl)
values = transcript_ids,
mart=ensembl,
verbose = FALSE)
names(data)<-c("geneID","geneName","chr","start","end","strand")
data <- data[c(3,4,5,6,1,2)]
if(length(data)>0){
hit<-stringr::str_detect(data$strand,"-1")
data$strand[hit]<-"-"
hit<-stringr::str_detect(data$strand,"1")
data$strand[hit]<-"+"
hit<-stringr::str_detect(data$chr,"CHR")==FALSE
data$chr[hit]<-paste("chr",data$chr[hit],sep = "")
}
return(data)
}
}else return(NULL)
}
filterGeneName<-function(genes,assembly,URL){
if(length(genes)!=0){
ensembl = returnEnsembl(assembly,URL)
gene_ids <- biomaRt::getBM(attributes = c("ensembl_gene_id", "hgnc_symbol"), filters = c("hgnc_symbol"), values = genes, mart = ensembl, verbose = T)
if(!is.null(ensembl) & !is.null(gene_ids)){
data <- getBM(attributes = c("ensembl_gene_id","external_gene_name",
"chromosome_name", "start_position", "end_position",
"strand"),
filters = c("ensembl_gene_id"), #listFilters(ensembl)
values = gene_ids$ensembl_gene_id,
mart=ensembl,
verbose = FALSE)
names(data)<-c("geneID","geneName","chr","start","end","strand")
data <- data[c(3,4,5,6,1,2)]
if(length(data)>0){
hit<-stringr::str_detect(data$strand,"-1")
data$strand[hit]<-"-"
hit<-stringr::str_detect(data$strand,"1")
data$strand[hit]<-"+"
hit<-stringr::str_detect(data$chr,"CHR")==FALSE
data$chr[hit]<-paste("chr",data$chr[hit],sep = "")
}
return(data)
}
}else return(NULL)
}
filterGeneID_V<-function(gene_ids,assembly,URL){
if(length(gene_ids)!=0){
ensembl = returnEnsembl(assembly,URL)
if(!is.null(ensembl) & !is.null(gene_ids)){
data <- biomaRt::getBM(attributes = c("ensembl_gene_id_version","external_gene_name",
"chromosome_name", "start_position", "end_position",
"strand"),
filters = c("ensembl_gene_id_version"), # listFilters(ensembl)
values = gene_ids,
mart=ensembl,
verbose = FALSE)
names(data)<-c("geneID","geneName","chr","start","end","strand")
data <- data[c(3,4,5,6,1,2)]
if(length(data)>0){
hit<-stringr::str_detect(data$strand,"-1")
data$strand[hit]<-"-"
hit<-stringr::str_detect(data$strand,"1")
data$strand[hit]<-"+"
hit<-stringr::str_detect(data$chr,"CHR")==FALSE
data$chr[hit]<-paste("chr",data$chr[hit],sep = "")
}
return(data)
}
}else return(NULL)
}
filterGeneID<-function(gene_ids,assembly,URL){
if(length(gene_ids)!=0){
ensembl = returnEnsembl(assembly,URL)
if(!is.null(ensembl) & !is.null(gene_ids)){
data <- biomaRt::getBM(attributes = c("ensembl_gene_id","external_gene_name",
"chromosome_name", "start_position", "end_position",
"strand"),
filters = c("ensembl_gene_id"), # listFilters(ensembl)
values = gene_ids,
mart=ensembl,
verbose = FALSE)
names(data)<-c("geneID","geneName","chr","start","end","strand")
data <- data[c(3,4,5,6,1,2)]
if(length(data)>0){
hit<-stringr::str_detect(data$strand,"-1")
data$strand[hit]<-"-"
hit<-stringr::str_detect(data$strand,"1")
data$strand[hit]<-"+"
hit<-stringr::str_detect(data$chr,"CHR")==FALSE
data$chr[hit]<-paste("chr",data$chr[hit],sep = "")
}
return(data)
}
}else return(NULL)
}
returnEnsembl<-function(assembly,URL){
if(assembly=="hg19" || assembly=="Grch37"){
ensembl = biomaRt::useEnsembl(biomart="ensembl", dataset="hsapiens_gene_ensembl", GRCh = 37, host = URL, verbose = TRUE)
return(ensembl)
}else if(assembly=="hg38" || assembly=="Grch38"){
ensembl = biomaRt::useEnsembl(biomart="ensembl", dataset="hsapiens_gene_ensembl", GRCh = 38, host = URL, verbose = TRUE)
return(ensembl)
}else if(assembly=="mm9" || assembly =="Grcm37"){
ensembl = biomaRt::useEnsembl(biomart="ensembl", dataset="mmusculus_gene_ensembl", host = URL, verbose = TRUE)
return(ensembl)
}else if(assembly=="mm10" || assembly =="Grcm38"){
ensembl = biomaRt::useEnsembl(biomart="ensembl", dataset="mmusculus_gene_ensembl", host = URL, verbose = TRUE)
return(ensembl)
}else if(assembly=="panTro4"){
ensembl = biomaRt::useEnsembl(biomart="ensembl", dataset="ptroglodytes_gene_ensembl", host = URL, verbose = TRUE)
return(ensembl)
}else if(assembly=="ponAbe2"){
ensembl = biomaRt::useEnsembl(biomart="ensembl", dataset="pabelii_gene_ensembl", host = URL, verbose = TRUE)
return(ensembl)
}else{
print("not found assembly")
return(NULL)}
}
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