Nothing
R/internal_dealWithGencode.R
In xQTLbiolinks: An R Package for Integrative Analysis of Quantitative Trait Locus Data of 'xQTL'
Defines functions
apiRef_gene
gtfSubsGene
gtfSubsGeneInfo
# @title download gtf files and extract gene info from attribute column:
#
# @param gencodeVersion "v26" or "v19"
#
# @return create .rds file
#
# @importFrom utils download.file
# @importFrom data.table fread rbindlist setnames as.data.table data.table
# @importFrom stringr str_split
gtfSubsGeneInfo <- function(gencodeVersion="v26"){
type <- NULL
gtfDir <- tempdir()
dir.create(gtfDir, recursive = TRUE)
message("created temp dir: ",gtfDir)
if(gencodeVersion=="v26" ){
gtfUrl <- paste0("http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_26/gencode.v26.annotation.gtf.gz")
utils::download.file(gtfUrl,paste0(gtfDir,"/gencode.annotation.gtf.gz"), method="curl")
# downloader::download(gtfUrl,paste0(gtfDir,"/gencode.annotation.gtf.gz"))
}
if(gencodeVersion=="v19"){
gtfUrl <- paste0("http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_19/gencode.v19.annotation.gtf.gz")
utils::download.file(gtfUrl,paste0(gtfDir,"/gencode.annotation.gtf.gz"), method="curl")
# downloader::download(gtfUrl,paste0(gtfDir,"/gencode.annotation.gtf.gz"))
}
# deal with gtf:
if( file.exists(paste0(gtfDir,"/gencode.annotation.gtf.gz")) ){
message(gtfDir,"/gencode.annotation.gtf.gz", " exists!")
# read gencode file:
gencodeAnno <- data.table::fread(paste0(gtfDir,"/gencode.annotation.gtf.gz"),sep="\t", header = FALSE)
data.table::setnames(gencodeAnno, names(gencodeAnno), c("chr","source","type","start","end","score","strand","phase","attributes") )
# for gene:
gencodeAnnoGene <- gencodeAnno[type == "gene"]
# use internal function: gtfSubsGene
gencodeENSG <- data.table::rbindlist(lapply(gencodeAnnoGene$attributes, gtfSubsGene, att_of_interest= c("gene_id", "gene_type", "gene_name")))
# gencodeENSG$ENSG <- unlist(lapply(gencodeENSG$gene_id, function(x){ str_split(x, fixed("."))[[1]][1] }))
if(gencodeVersion=="v26"){
rowRange1 <- c(seq(from=1, to=nrow(gencodeENSG), by=200), nrow(gencodeENSG))
gencodeGeneInfoV26 <- data.table::data.table()
for(i in 1:(length(rowRange1)-1)){
# use internal function: apiRef_gene
apiRef_geneOut_tmp = apiRef_gene( gencodeENSG[rowRange1[i]:(rowRange1[i+1]-1),]$gene_id, "v26", "GRCh38/hg38")
gencodeGeneInfoV26 <- rbind(gencodeGeneInfoV26, apiRef_geneOut_tmp)
rm(apiRef_geneOut_tmp)
message(i,"/",(length(rowRange1)-1), "; Complete ", round(i/(length(rowRange1)-1)*100,2),"%")
}
# add last row:
apiRef_geneOut_tmp = apiRef_gene( gencodeENSG[rowRange1[length(rowRange1)],]$gene_id, "v26", "GRCh38/hg38")
gencodeGeneInfoV26 <- rbind(gencodeGeneInfoV26, apiRef_geneOut_tmp)
rm(apiRef_geneOut_tmp)
# create .rds file with gencodeGeneInfoV26
# usethis::use_data(gencodeGeneInfoV26)
}
if(gencodeVersion=="v19"){
rowRange1 <- c(seq(from=1, to=nrow(gencodeENSG), by=200), nrow(gencodeENSG))
gencodeGeneInfoV19 <- data.table::data.table()
for(i in 1:(length(rowRange1)-1)){
# use internal function: apiRef_gene
apiRef_geneOut_tmp = apiRef_gene( gencodeENSG[rowRange1[i]:(rowRange1[i+1]-1),]$gene_id, "v19", "GRCh37/hg19")
gencodeGeneInfoV19 <- rbind(gencodeGeneInfoV19, apiRef_geneOut_tmp)
rm(apiRef_geneOut_tmp)
message(i,"/",(length(rowRange1)-1), "; Complete ", round(i/(length(rowRange1)-1)*100,2),"%")
}
# add last row:
apiRef_geneOut_tmp = apiRef_gene( gencodeENSG[rowRange1[length(rowRange1)],]$gene_id, "v19", "GRCh37/hg19")
gencodeGeneInfoV19 <- rbind(gencodeGeneInfoV19, apiRef_geneOut_tmp)
rm(apiRef_geneOut_tmp)
# create .rds file with gencodeGeneInfoV19
# usethis::use_data(gencodeGeneInfoV19, overwrite = TRUE)
}
}
return(NULL)
}
# @title Extract gene attributes of interest
# @description
# as a funciton of lapply
# @param gtf_attributes A character string or a character vector. Like: c("gene_id", "gene_type", "gene_name"). Default: "gene_id", "gene_type", "gene_name".
# @param att_of_interest A character string or a character vector. Attributes of interest.
#
# @return specificed attributes
# @importFrom data.table as.data.table
# @examples
# \dontrun{
# # extract gene info:
# gencodeENSG <- data.table::rbindlist(lapply(gencodeAnnoGene$attributes,
# gtfSubsGene,
# c("gene_id", "gene_type", "gene_name")))
# # extract transcript info:
# gencodeENSG <- data.table::rbindlist(lapply(gencodeAnnoGene$attributes,
# gtfSubsGene,
# c("gene_id","transcript_id",
# "gene_type", "gene_name")))
# }
gtfSubsGene <- function(gtf_attributes, att_of_interest= c("gene_id", "gene_type", "gene_name")){
att <- unlist(stringr::str_split(gtf_attributes, " ")[[1]])
# att_of_interest <- c("gene_id", "gene_type", "gene_name")
if(any(att_of_interest %in% att)){
dt <- data.table::as.data.table(matrix(gsub("\"|;","", att[which(att %in% att_of_interest)+1]),nrow=1))
names(dt) <- att_of_interest
return( dt )
}else{
return(NA)}
}
# @title fetch reference genes by API.
#
# @param geneId a character or a character vector(versioned ensemble ID or unversioned ensemble ID)
# @param gencodeVersion "v26" or "v19"
# @param genomeBuild "GRCh38/hg38" or "GRCh37/hg19"
#
# @return queried gene info table
# @importFrom jsonlite fromJSON
# @importFrom data.table as.data.table
# @examples
# # apiRef_gene(c("ENSG00000116885.18","ENSG00000222623"), "v26", "GRCh38/hg38")
apiRef_gene <- function(geneId="", gencodeVersion="v26", genomeBuild="GRCh38/hg38" ){
geneSymbol <- gencodeId <- entrezGeneId <- geneType <- chromosome <- start <- end <- strand <- tss <- description <- NULL
.<-NULL
geneId <- as.character(unlist(geneId))
if( any(is.na(geneId)) | any(geneId=="") | any(is.null(geneId)) ){
stop("gene ID can not be null!")
}else if(length(geneId)>200){
stop("number of gene ID can not > 200 ")
}else{
url1 <- paste0("https://gtexportal.org/rest/v1/reference/gene?",
"geneId=", paste0(geneId, collapse = ","),"&",
"gencodeVersion=", gencodeVersion,"&",
"genomeBuild=",genomeBuild,"&",
"page=0&pageSize=2000&format=json"
)
# use internal function: apiAdmin_ping
# check network:
bestFetchMethod <- apiAdmin_ping()
if( !exists("bestFetchMethod") || is.null(bestFetchMethod) ){
message("Note: API server is busy or your network has latency, please try again later.")
return(NULL)
}
message("GTEx API successfully accessed!")
# url1Get <- httr::GET(url1, httr::progress())
url1GetText2Json <- fetchContent(url1, method = bestFetchMethod[1], downloadMethod = bestFetchMethod[2])
url1GetText2Json2DT <- data.table::as.data.table(url1GetText2Json$gene)
url1GetText2Json2DT$genomeBuild <- genomeBuild
outInfo <- url1GetText2Json2DT[,.(geneSymbol, gencodeId, entrezGeneId, geneType, chromosome, start, end, strand, tss, gencodeVersion,genomeBuild, description)]
return(outInfo)
}
}
# @title create .rds file with xQTLquery_sample function
#
# @param datasetId "gtex_v8" or "gtex_v7"
#
# @return none
createTissueSiteDetailMappingData <- function(datasetId="gtex_v8"){
# tissueSiteDetail <- tissueSiteDetailId <- NULL
# .<-NULL
# # obtain all tissueSiteDetail info:
# if( datasetId == "gtex_v8" ){
# tissueSiteDetailGTExv8 <- xQTLquery_sample( tissueSiteDetail="All", dataType="RNASEQ", datasetId="gtex_v8",recordPerChunk =2000 )
# tissueSiteDetailGTExv8 <- unique(tissueSiteDetailGTExv8[,.(tissueSiteDetail,tissueSiteDetailId)][order(tissueSiteDetail)])
# usethis::use_data(tissueSiteDetailGTExv8, overwrite = TRUE)
# }else if(datasetId == "gtex_v7" ){
# tissueSiteDetailGTExv7 <- xQTLquery_sample( tissueSiteDetail="All", dataType="RNASEQ", datasetId="gtex_v7",recordPerChunk =2000 )
# tissueSiteDetailGTExv7 <- unique(tissueSiteDetailGTExv7[,.(tissueSiteDetail,tissueSiteDetailId)][order(tissueSiteDetail)])
# usethis::use_data(tissueSiteDetailGTExv7, overwrite = TRUE)
# }
#
# url1 <- "https://gtexportal.org/rest/v1/dataset/tissueInfo?format=json&datasetId=gtex_v8"
# url1 <- utils::URLencode(url1)
# url1GetText2Json <- fetchContent(url1, method = "curl", downloadMethod = bestFetchMethod[2])
# outInfo <- data.table::as.data.table(url1GetText2Json$tissueInfo)
# tissueSiteDetailGTExv8 <- outInfo[,.(tissueSiteDetail, tissueSiteDetailId, tissueSite)]
# usethis::use_data(tissueSiteDetailGTExv8, overwrite = TRUE)
#
# url1 <- "https://gtexportal.org/rest/v1/dataset/tissueInfo?format=json&datasetId=gtex_v7"
# url1 <- utils::URLencode(url1)
# url1GetText2Json <- fetchContent(url1, method = "curl", downloadMethod = bestFetchMethod[2])
# outInfo <- data.table::as.data.table(url1GetText2Json$tissueInfo)
# tissueSiteDetailGTExv7 <- outInfo[,.(tissueSiteDetail, tissueSiteDetailId, tissueSite)]
# usethis::use_data(tissueSiteDetailGTExv7, overwrite = TRUE)
return(NULL)
}
# @title Query gene information through all genes' information
# @description
# users can use this function to search gene of interest
# @param genes Following gene types are supported:
# \itemize{
# \item \strong{Gene symbol}.
#
# A character string or a character vector (case ignored). like: "tp53","naDK","SDF4".
# \item \strong{Gencode/ensemble id} (versioned or unversioned).
#
# A character string or a character vector (case ignored). like: "ENSG00000210195.2","ENSG00000078808".
# \item \strong{Entrez gene ID}.
#
# A integer string or a integer vectors. like: 51150,5590,4509.
#
# \item \strong{geneCategory}.
#
# When choose "geneCategory", "genes" must be chosen from following gene category:
# \itemize{
# \item protein coding
# \item antisense
# \item lincRNA
# \item unprocessed pseudogene
# \item miRNA
# \item transcribed unprocessed pseudogene
# \item snRNA
# \item processed pseudogene
# \item processed transcript
# \item TEC
# \item transcribed unitary pseudogene
# \item transcribed processed pseudogene
# \item sense intronic
# \item misc RNA
# \item snoRNA
# \item scaRNA
# \item rRNA
# \item unitary pseudogene
# \item 3prime overlapping ncRNA
# \item polymorphic pseudogene
# \item bidirectional promoter lncRNA
# \item sense overlapping
# \item pseudogene
# \item IG V pseudogene
# \item scRNA
# \item IG C gene
# \item IG J gene
# \item IG V gene
# \item sRNA
# \item ribozyme
# \item vaultRNA
# \item non coding
# \item TR J gene
# \item TR C gene
# \item TR V gene
# \item TR V pseudogene
# \item TR D gene
# \item IG C pseudogene
# \item macro lncRNA
# \item TR J pseudogene
# \item IG D gene
# \item IG J pseudogene
# \item IG pseudogene
# \item Mt tRNA
# \item Mt rRNA
# }
# }
#
# @param geneType A character string. Types of queried genes. Options: "geneSymbol" (default), "gencodeId", "entrezId";
# @param gencodeVersion A character string. Two version are supported: "v26" (default) and "v19"
# @param genomeBuild A character string. "GRCh38/hg38"(default) for gencodeVersion "v26", "GRCh37/hg19" for gencodeVersion "v19"
# @import data.table
# @import stringr
# @return A data.table of queried gene information. including following columns:
# \itemize{
# \item \strong{genes.} Input genes
# \item \strong{geneSymbol.} Gene symbol.
# \item \strong{gencodeId.} Gencode/ensemble id (versioned).
# \item \strong{entrezGeneId.} Entrez gene ID.
# \item \strong{geneType.} Gene type.
# \item \strong{chromosome.} Note: "chr" is added in gencode v26,
# \item \strong{start.}
# \item \strong{end.}
# \item \strong{strand.}
# \item \strong{tss.} Transcriptional start site.
# \item \strong{gencodeVersion.} Gencode Version.
# \item \strong{genomeBuild.} Genome version.
# \item \strong{description.}
# }
apiRef_genes <- function(genes="", geneType="geneSymbol", gencodeVersion="v26", genomeBuild="GRCh38/hg38"){
# check null/na
if( is.null(genes) || any(is.na(genes)) || any(genes=="") ||length(genes)==0 ){
stop("Parameter \"genes\" can not be NULL or NA!")
}
# geneType
if( is.null(geneType) || any(is.na(geneType)) || any(geneType=="") || length(geneType)!=1){
stop("Parameter \"geneType\" should be choosen from \"geneSymbol\", \"gencodeId\", \"entrezId\".")
}else if( !(geneType %in% c("geneSymbol", "gencodeId", "entrezId","geneCategory")) ){
stop("Parameter \"geneType\" should be choosen from \"geneSymbol\", \"gencodeId\", \"entrezId\",\"geneCategory\".")
}
# gencodeVersion
if( is.null(gencodeVersion) || any(is.na(gencodeVersion)) || any(gencodeVersion=="") || length(gencodeVersion)!=1){
stop("Parameter \"gencodeVersion\" should be choosen from \"v26\", \"v19\".")
}else if( !(gencodeVersion %in% c("v26", "v19")) ){
stop("Parameter \"gencodeVersion\" should be choosen from \"v26\", \"v19\".")
}
# genomeBuild
# check gencodeVersion match with genomeBuild
if( is.null(genomeBuild) || any(is.na(genomeBuild)) || any(genomeBuild=="") || length(genomeBuild)!=1){
stop("Parameter \"genomeBuild\" should be choosen from \"GRCh38/hg38\", \"GRCh37/hg19\".")
}else if( !(genomeBuild %in% c("GRCh38/hg38", "GRCh37/hg19")) ){
stop("Parameter \"genomeBuild\" should be choosen from \"GRCh38/hg38\", \"GRCh37/hg19\".")
} else if(gencodeVersion=="v26" & genomeBuild=="GRCh38/hg38"){
# data(gencodeGeneInfoV26)
# gencodeGeneInfo <- data.table::copy(gencodeGeneInfoV26)
gencodeGeneInfo <- xQTLquery_geneAll("v26")
}else if(gencodeVersion=="v19" & genomeBuild=="GRCh37/hg19"){
# data(gencodeGeneInfoV19)
# gencodeGeneInfo <- data.table::copy(gencodeGeneInfoV19)
gencodeGeneInfo <- xQTLquery_geneAll("v19")
}else{
stop("gencodeVersion must be matched with genomeBuild.\n eg. v26(GRCh38/hg38), v19(GRCh37/hg19)")
}
# merge:
if( geneType=="geneSymbol" ){
genesDT <- data.table::data.table(genes=as.character(genes))
genesDT$geneSymbolUpper <- toupper(genesDT$genes)
gencodeGeneInfo$geneSymbolUpper<- toupper(gencodeGeneInfo$geneSymbol)
genesDTout <- merge(genesDT, gencodeGeneInfo, by ="geneSymbolUpper", sort=FALSE)
genesDTout <- genesDTout[,-c("geneSymbolUpper")]
if( nrow(genesDTout) >0){
if( length(genes)>1 ){
message("Queried ",length(genes), " genes, finally ",nrow(genesDTout)," records matched!")
}else if( length(genes)==1 ){
message("Queried ",length(genes), " gene, finally ",nrow(genesDTout)," record matched!")
}
return(genesDTout)
}else{
if( length(genes)>1 ){
message("Queried ",length(genes), " genes, finally 0 record matched!\nplease check your input genes!")
}else if( length(genes)==1 ){
message("Queried ",length(genes), " gene, finally 0 record matched!\nplease check your input genes!")
}
return(data.table::data.table(genes=genes))
}
}
# gencodeId
if( geneType=="gencodeId" ){
genesDT <- data.table::data.table(genes=as.character(genes))
genesDT$gencodeIdUpper <- toupper(genesDT$genes)
gencodeGeneInfo$gencodeIdUpper<- toupper(gencodeGeneInfo$gencodeId)
gencodeGeneInfo$gencodIdUv <- unlist(lapply(gencodeGeneInfo$gencodeId, function(x){ stringr::str_split_fixed(x, stringr::fixed("."),2)[1] }))
gencodeGeneInfo$gencodIdUvUpper<- toupper(gencodeGeneInfo$gencodIdUv)
genesDTout_1 <- merge(genesDT, gencodeGeneInfo, by ="gencodeIdUpper", sort=FALSE)
genesDTout_2 <- merge( gencodeGeneInfo, genesDT, by.y ="gencodeIdUpper", by.x= "gencodIdUvUpper", sort=FALSE)
genesDTout <- rbind(genesDTout_1, genesDTout_2)[,c("genes",names(gencodeGeneInfo[,-c("gencodeIdUpper", "gencodIdUv", "gencodIdUvUpper")])),with=FALSE]
if( nrow(genesDTout) >0){
message("Queried ",length(genes), " genes, finally ",nrow(genesDTout)," records matched!")
return(genesDTout)
}else{
message("Queried ",length(genes), " genes, finally 0 records matched!\nplease check your input genes!")
return(data.table::data.table(genes=genes))
}
# entrezId
}else if( geneType=="entrezId" ){
if( !all(unlist(lapply(genes, is.numeric))) ){
stop("Integer is requeried for entrezId!")
}
genesDT <- data.table::data.table(genes=genes)
gencodeGeneInfo$genes <- gencodeGeneInfo$entrezGeneId
genesDTout <- merge(genesDT, gencodeGeneInfo, by ="genes", sort=FALSE)
if( nrow(genesDTout) >0){
message("Queried ",length(genes), " genes, finally ",nrow(genesDTout)," records matched!")
return(genesDTout)
}else{
message("Queried ",length(genes), " genes, finally 0 records matched!\nplease check your input genes!")
return(data.table::data.table(genes=genes))
}
# geneCategory
}else if(geneType == "geneCategory"){
geneCategory = unique(gencodeGeneInfo$geneType)
if( length(genes)!=1 || any(!(genes %in% geneCategory)) ){
message(paste0(1:length(geneCategory),". ",geneCategory, collapse = "\n"))
stop("if \"geneType\" is \"geneCategory\", input \"genes\" should be choosen from the above: ")
}else{
genesDTout <- cbind(data.table(genes=gencodeGeneInfo[geneType==genes,]$geneSymbol), gencodeGeneInfo[geneType==genes,])
return(genesDTout)
}
}else{
return(data.table::data.table(genes=genes))
}
}
# @title Create gene annotation data
# @import data.table
# @import stringr
# @return NULL
createGencodeGeneInfoAll <- function(){
gencodeId <- chromosome <- strand <- gencodeId_unversioned <- startV26 <- startV19 <- NULL
.<-NULL
# # 生成 gencodeGeneInfoAllGranges
gencodeGeneInfoV26<- xQTLquery_geneAll("v26")
gencodeGeneInfoV19<- xQTLquery_geneAll("v19")
gencodeGeneInfoV26<- gencodeGeneInfoV26[,.(gencodeId, chromosome, start, end, strand, gencodeId_unversioned= unlist(lapply(gencodeId, function(x){str_split(x, fixed("."))[[1]][1]})))]
gencodeGeneInfoV19 <- gencodeGeneInfoV19[,.(gencodeId, chromosome=paste0("chr",chromosome), start, end, strand, gencodeId_unversioned =unlist(lapply(gencodeId, function(x){str_split(x, fixed("."))[[1]][1]})) )]
gencodeGeneInfoAll <- merge(gencodeGeneInfoV26[,.(gencodeId, gencodeId_unversioned, chromosome, strand, start, end)], gencodeGeneInfoV19[,.(gencodeId, gencodeId_unversioned, chromosome, strand, start, end)], by=c("gencodeId_unversioned", "chromosome", "strand"), all=TRUE, suffixes=c("V26","V19"))
gencodeGeneInfoAll <- gencodeGeneInfoAll[chromosome %in% paste0("chr",c(1:22,"X", "Y")),][order(chromosome, -startV26, -startV19)]
gencodeGeneInfoAllGranges <- GenomicRanges::GRanges(ifelse(is.na(gencodeGeneInfoAll$chromosome),"NA",gencodeGeneInfoAll$chromosome),
IRanges::IRanges(ifelse(is.na(gencodeGeneInfoAll$startV26),-1,gencodeGeneInfoAll$startV26), ifelse(is.na(gencodeGeneInfoAll$endV26),-1,gencodeGeneInfoAll$endV26)),
strand= ifelse(is.na(gencodeGeneInfoAll$strand),"*",gencodeGeneInfoAll$strand)
)
gencodeGeneInfoAllGranges$rangesV19 <- IRanges::IRanges(ifelse(is.na(gencodeGeneInfoAll$startV19),-1,gencodeGeneInfoAll$startV19), ifelse(is.na(gencodeGeneInfoAll$endV19),-1,gencodeGeneInfoAll$endV19))
gencodeGeneInfoAllGranges$gencodeId <- gencodeGeneInfoAll$gencodeId_unversioned
usethis::use_data(gencodeGeneInfoAllGranges, overwrite = TRUE)
# # usethis::use_data(gencodeGeneInfoAll, overwrite = TRUE)
return(NULL)
}
# httr::use_proxy(url="127.0.0.1", port=7890
# # ,username="dd",password="123456"
# )
# devtools::build("D:/R_project/GTExbiolinks","D:/R_project/GTExbiolinks.tar.gz")
#
# install.packages("~/GTExbiolinks.tar.gz", repos = NULL, type = "source")
# install.packages("~/GTExbiolinks.tar.gz", repos = NULL, type = "source", lib="/home/dingruofan/anaconda3/envs/work/lib/R/library")
# install.packages("~/GTExbiolinks_0.0.0.9000.tar.gz", repos = NULL, type = "source", lib="/home/dingruofan/anaconda3/envs/work/lib/R/library")
# import:
# usethis::use_package("data.table",min_version ="1.14.2")
# usethis::use_package("curl", min_version = "4.3.2")
# usethis::use_package("jsonlite", min_version = "1.7.2")
# usethis::use_package("stringr", min_version = "1.4.0")
# usethis::use_package("utils", min_version = "4.0.3")
# usethis::use_package("SummarizedExperiment", min_version = "1.18.2")
# usethis::use_package("ggplot2", min_version = "3.3.5")
# usethis::use_package("httr", min_version = "1.4.2")
# usethis::use_package("RMySQL", min_version = "0.10.22")
# usethis::use_package("DBI", min_version = "1.1.1") # in RMySQL
# usethis::use_package("PupillometryR", min_version = "0.0.4")
# usethis::use_package("ggpubr", min_version = "0.4.0")
# usethis::use_package("GenomeInfoDb", min_version = "1.24.2") # in GenomicRanges
# usethis::use_package("IRanges", min_version = "2.22.2") # in GenomicRanges
# usethis::use_package("ggrepel", min_version = "0.9.1") # in ggpubr
# usethis::use_package("coloc", min_version = "5.1.0")
# usethis::use_package("GenomicRanges", min_version = "1.40.0") # in SummarizedExperiment
# no version info:
# usethis::use_package("data.table",min_version ="1.14.2")
# usethis::use_package("curl", min_version = "4.3.2")
# usethis::use_package("jsonlite", min_version = "1.7.2")
# usethis::use_package("stringr", min_version = "1.4.0")
# usethis::use_package("utils", min_version = "4.0.3")
# usethis::use_package("SummarizedExperiment", min_version = "1.4.0")
# usethis::use_package("ggplot2", min_version="3.3.6")
# usethis::use_package("RMySQL")
# usethis::use_package("DBI") # in RMySQL
# usethis::use_package("ggridges")
# usethis::use_package("viridis")
# usethis::use_package("GenomeInfoDb") # in GenomicRanges
# usethis::use_package("IRanges") # in GenomicRanges
# usethis::use_package("ggrepel") # in ggpubr
# usethis::use_package("GenomicRanges") # in SummarizedExperiment
# usethis::use_package("BiocGenerics")
# usethis::use_package("cowplot", min_version="1.1.1")
# usethis::use_package("GenomicFeatures")
# usethis::use_package("VariantAnnotation")
# usethis::use_package("TxDb.Hsapiens.UCSC.hg38.knownGene")
# usethis::use_package("SummarizedExperiment")
#
# # suggest:
# usethis::use_package("usethis", type="Suggests")
# usethis::use_package("knitr", type="Suggests")
# usethis::use_package("rtracklayer",type="Suggests")
# usethis::use_package("coloc",type="Suggests")
# usethis::use_package("hyprcoloc",type="Suggests")
# usethis::use_package("PupillometryR")
# usethis::use_package("ggridges", type="Suggests")
# usethis::use_package("viridis", type="Suggests")
# usethis::use_package("crayon", min_version = "1.4.1") # message 字体：
# usethis::use_package("ggeextra", min_version = "1.4.1") # message 字体：
# usethis::use_package("rlang", min_version = "0.4.11", type="Suggests") # in ggpubr
# usethis::use_package("httr")
# usethis::use_package("scales")
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xQTLbiolinks documentation built on Sept. 15, 2023, 1:06 a.m.
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Defines functions apiRef_gene gtfSubsGene gtfSubsGeneInfo
# @title download gtf files and extract gene info from attribute column:
#
# @param gencodeVersion "v26" or "v19"
#
# @return create .rds file
#
# @importFrom utils download.file
# @importFrom data.table fread rbindlist setnames as.data.table data.table
# @importFrom stringr str_split
gtfSubsGeneInfo <- function(gencodeVersion="v26"){
type <- NULL
gtfDir <- tempdir()
dir.create(gtfDir, recursive = TRUE)
message("created temp dir: ",gtfDir)
if(gencodeVersion=="v26" ){
gtfUrl <- paste0("http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_26/gencode.v26.annotation.gtf.gz")
utils::download.file(gtfUrl,paste0(gtfDir,"/gencode.annotation.gtf.gz"), method="curl")
# downloader::download(gtfUrl,paste0(gtfDir,"/gencode.annotation.gtf.gz"))
}
if(gencodeVersion=="v19"){
gtfUrl <- paste0("http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_19/gencode.v19.annotation.gtf.gz")
utils::download.file(gtfUrl,paste0(gtfDir,"/gencode.annotation.gtf.gz"), method="curl")
# downloader::download(gtfUrl,paste0(gtfDir,"/gencode.annotation.gtf.gz"))
}
# deal with gtf:
if( file.exists(paste0(gtfDir,"/gencode.annotation.gtf.gz")) ){
message(gtfDir,"/gencode.annotation.gtf.gz", " exists!")
# read gencode file:
gencodeAnno <- data.table::fread(paste0(gtfDir,"/gencode.annotation.gtf.gz"),sep="\t", header = FALSE)
data.table::setnames(gencodeAnno, names(gencodeAnno), c("chr","source","type","start","end","score","strand","phase","attributes") )
# for gene:
gencodeAnnoGene <- gencodeAnno[type == "gene"]
# use internal function: gtfSubsGene
gencodeENSG <- data.table::rbindlist(lapply(gencodeAnnoGene$attributes, gtfSubsGene, att_of_interest= c("gene_id", "gene_type", "gene_name")))
# gencodeENSG$ENSG <- unlist(lapply(gencodeENSG$gene_id, function(x){ str_split(x, fixed("."))[[1]][1] }))
if(gencodeVersion=="v26"){
rowRange1 <- c(seq(from=1, to=nrow(gencodeENSG), by=200), nrow(gencodeENSG))
gencodeGeneInfoV26 <- data.table::data.table()
for(i in 1:(length(rowRange1)-1)){
# use internal function: apiRef_gene
apiRef_geneOut_tmp = apiRef_gene( gencodeENSG[rowRange1[i]:(rowRange1[i+1]-1),]$gene_id, "v26", "GRCh38/hg38")
gencodeGeneInfoV26 <- rbind(gencodeGeneInfoV26, apiRef_geneOut_tmp)
rm(apiRef_geneOut_tmp)
message(i,"/",(length(rowRange1)-1), "; Complete ", round(i/(length(rowRange1)-1)*100,2),"%")
}
# add last row:
apiRef_geneOut_tmp = apiRef_gene( gencodeENSG[rowRange1[length(rowRange1)],]$gene_id, "v26", "GRCh38/hg38")
gencodeGeneInfoV26 <- rbind(gencodeGeneInfoV26, apiRef_geneOut_tmp)
rm(apiRef_geneOut_tmp)
# create .rds file with gencodeGeneInfoV26
# usethis::use_data(gencodeGeneInfoV26)
}
if(gencodeVersion=="v19"){
rowRange1 <- c(seq(from=1, to=nrow(gencodeENSG), by=200), nrow(gencodeENSG))
gencodeGeneInfoV19 <- data.table::data.table()
for(i in 1:(length(rowRange1)-1)){
# use internal function: apiRef_gene
apiRef_geneOut_tmp = apiRef_gene( gencodeENSG[rowRange1[i]:(rowRange1[i+1]-1),]$gene_id, "v19", "GRCh37/hg19")
gencodeGeneInfoV19 <- rbind(gencodeGeneInfoV19, apiRef_geneOut_tmp)
rm(apiRef_geneOut_tmp)
message(i,"/",(length(rowRange1)-1), "; Complete ", round(i/(length(rowRange1)-1)*100,2),"%")
}
# add last row:
apiRef_geneOut_tmp = apiRef_gene( gencodeENSG[rowRange1[length(rowRange1)],]$gene_id, "v19", "GRCh37/hg19")
gencodeGeneInfoV19 <- rbind(gencodeGeneInfoV19, apiRef_geneOut_tmp)
rm(apiRef_geneOut_tmp)
# create .rds file with gencodeGeneInfoV19
# usethis::use_data(gencodeGeneInfoV19, overwrite = TRUE)
}
}
return(NULL)
}
# @title Extract gene attributes of interest
# @description
# as a funciton of lapply
# @param gtf_attributes A character string or a character vector. Like: c("gene_id", "gene_type", "gene_name"). Default: "gene_id", "gene_type", "gene_name".
# @param att_of_interest A character string or a character vector. Attributes of interest.
#
# @return specificed attributes
# @importFrom data.table as.data.table
# @examples
# \dontrun{
# # extract gene info:
# gencodeENSG <- data.table::rbindlist(lapply(gencodeAnnoGene$attributes,
# gtfSubsGene,
# c("gene_id", "gene_type", "gene_name")))
# # extract transcript info:
# gencodeENSG <- data.table::rbindlist(lapply(gencodeAnnoGene$attributes,
# gtfSubsGene,
# c("gene_id","transcript_id",
# "gene_type", "gene_name")))
# }
gtfSubsGene <- function(gtf_attributes, att_of_interest= c("gene_id", "gene_type", "gene_name")){
att <- unlist(stringr::str_split(gtf_attributes, " ")[[1]])
# att_of_interest <- c("gene_id", "gene_type", "gene_name")
if(any(att_of_interest %in% att)){
dt <- data.table::as.data.table(matrix(gsub("\"|;","", att[which(att %in% att_of_interest)+1]),nrow=1))
names(dt) <- att_of_interest
return( dt )
}else{
return(NA)}
}
# @title fetch reference genes by API.
#
# @param geneId a character or a character vector(versioned ensemble ID or unversioned ensemble ID)
# @param gencodeVersion "v26" or "v19"
# @param genomeBuild "GRCh38/hg38" or "GRCh37/hg19"
#
# @return queried gene info table
# @importFrom jsonlite fromJSON
# @importFrom data.table as.data.table
# @examples
# # apiRef_gene(c("ENSG00000116885.18","ENSG00000222623"), "v26", "GRCh38/hg38")
apiRef_gene <- function(geneId="", gencodeVersion="v26", genomeBuild="GRCh38/hg38" ){
geneSymbol <- gencodeId <- entrezGeneId <- geneType <- chromosome <- start <- end <- strand <- tss <- description <- NULL
.<-NULL
geneId <- as.character(unlist(geneId))
if( any(is.na(geneId)) | any(geneId=="") | any(is.null(geneId)) ){
stop("gene ID can not be null!")
}else if(length(geneId)>200){
stop("number of gene ID can not > 200 ")
}else{
url1 <- paste0("https://gtexportal.org/rest/v1/reference/gene?",
"geneId=", paste0(geneId, collapse = ","),"&",
"gencodeVersion=", gencodeVersion,"&",
"genomeBuild=",genomeBuild,"&",
"page=0&pageSize=2000&format=json"
)
# use internal function: apiAdmin_ping
# check network:
bestFetchMethod <- apiAdmin_ping()
if( !exists("bestFetchMethod") || is.null(bestFetchMethod) ){
message("Note: API server is busy or your network has latency, please try again later.")
return(NULL)
}
message("GTEx API successfully accessed!")
# url1Get <- httr::GET(url1, httr::progress())
url1GetText2Json <- fetchContent(url1, method = bestFetchMethod[1], downloadMethod = bestFetchMethod[2])
url1GetText2Json2DT <- data.table::as.data.table(url1GetText2Json$gene)
url1GetText2Json2DT$genomeBuild <- genomeBuild
outInfo <- url1GetText2Json2DT[,.(geneSymbol, gencodeId, entrezGeneId, geneType, chromosome, start, end, strand, tss, gencodeVersion,genomeBuild, description)]
return(outInfo)
}
}
# @title create .rds file with xQTLquery_sample function
#
# @param datasetId "gtex_v8" or "gtex_v7"
#
# @return none
createTissueSiteDetailMappingData <- function(datasetId="gtex_v8"){
# tissueSiteDetail <- tissueSiteDetailId <- NULL
# .<-NULL
# # obtain all tissueSiteDetail info:
# if( datasetId == "gtex_v8" ){
# tissueSiteDetailGTExv8 <- xQTLquery_sample( tissueSiteDetail="All", dataType="RNASEQ", datasetId="gtex_v8",recordPerChunk =2000 )
# tissueSiteDetailGTExv8 <- unique(tissueSiteDetailGTExv8[,.(tissueSiteDetail,tissueSiteDetailId)][order(tissueSiteDetail)])
# usethis::use_data(tissueSiteDetailGTExv8, overwrite = TRUE)
# }else if(datasetId == "gtex_v7" ){
# tissueSiteDetailGTExv7 <- xQTLquery_sample( tissueSiteDetail="All", dataType="RNASEQ", datasetId="gtex_v7",recordPerChunk =2000 )
# tissueSiteDetailGTExv7 <- unique(tissueSiteDetailGTExv7[,.(tissueSiteDetail,tissueSiteDetailId)][order(tissueSiteDetail)])
# usethis::use_data(tissueSiteDetailGTExv7, overwrite = TRUE)
# }
#
# url1 <- "https://gtexportal.org/rest/v1/dataset/tissueInfo?format=json&datasetId=gtex_v8"
# url1 <- utils::URLencode(url1)
# url1GetText2Json <- fetchContent(url1, method = "curl", downloadMethod = bestFetchMethod[2])
# outInfo <- data.table::as.data.table(url1GetText2Json$tissueInfo)
# tissueSiteDetailGTExv8 <- outInfo[,.(tissueSiteDetail, tissueSiteDetailId, tissueSite)]
# usethis::use_data(tissueSiteDetailGTExv8, overwrite = TRUE)
#
# url1 <- "https://gtexportal.org/rest/v1/dataset/tissueInfo?format=json&datasetId=gtex_v7"
# url1 <- utils::URLencode(url1)
# url1GetText2Json <- fetchContent(url1, method = "curl", downloadMethod = bestFetchMethod[2])
# outInfo <- data.table::as.data.table(url1GetText2Json$tissueInfo)
# tissueSiteDetailGTExv7 <- outInfo[,.(tissueSiteDetail, tissueSiteDetailId, tissueSite)]
# usethis::use_data(tissueSiteDetailGTExv7, overwrite = TRUE)
return(NULL)
}
# @title Query gene information through all genes' information
# @description
# users can use this function to search gene of interest
# @param genes Following gene types are supported:
# \itemize{
# \item \strong{Gene symbol}.
#
# A character string or a character vector (case ignored). like: "tp53","naDK","SDF4".
# \item \strong{Gencode/ensemble id} (versioned or unversioned).
#
# A character string or a character vector (case ignored). like: "ENSG00000210195.2","ENSG00000078808".
# \item \strong{Entrez gene ID}.
#
# A integer string or a integer vectors. like: 51150,5590,4509.
#
# \item \strong{geneCategory}.
#
# When choose "geneCategory", "genes" must be chosen from following gene category:
# \itemize{
# \item protein coding
# \item antisense
# \item lincRNA
# \item unprocessed pseudogene
# \item miRNA
# \item transcribed unprocessed pseudogene
# \item snRNA
# \item processed pseudogene
# \item processed transcript
# \item TEC
# \item transcribed unitary pseudogene
# \item transcribed processed pseudogene
# \item sense intronic
# \item misc RNA
# \item snoRNA
# \item scaRNA
# \item rRNA
# \item unitary pseudogene
# \item 3prime overlapping ncRNA
# \item polymorphic pseudogene
# \item bidirectional promoter lncRNA
# \item sense overlapping
# \item pseudogene
# \item IG V pseudogene
# \item scRNA
# \item IG C gene
# \item IG J gene
# \item IG V gene
# \item sRNA
# \item ribozyme
# \item vaultRNA
# \item non coding
# \item TR J gene
# \item TR C gene
# \item TR V gene
# \item TR V pseudogene
# \item TR D gene
# \item IG C pseudogene
# \item macro lncRNA
# \item TR J pseudogene
# \item IG D gene
# \item IG J pseudogene
# \item IG pseudogene
# \item Mt tRNA
# \item Mt rRNA
# }
# }
#
# @param geneType A character string. Types of queried genes. Options: "geneSymbol" (default), "gencodeId", "entrezId";
# @param gencodeVersion A character string. Two version are supported: "v26" (default) and "v19"
# @param genomeBuild A character string. "GRCh38/hg38"(default) for gencodeVersion "v26", "GRCh37/hg19" for gencodeVersion "v19"
# @import data.table
# @import stringr
# @return A data.table of queried gene information. including following columns:
# \itemize{
# \item \strong{genes.} Input genes
# \item \strong{geneSymbol.} Gene symbol.
# \item \strong{gencodeId.} Gencode/ensemble id (versioned).
# \item \strong{entrezGeneId.} Entrez gene ID.
# \item \strong{geneType.} Gene type.
# \item \strong{chromosome.} Note: "chr" is added in gencode v26,
# \item \strong{start.}
# \item \strong{end.}
# \item \strong{strand.}
# \item \strong{tss.} Transcriptional start site.
# \item \strong{gencodeVersion.} Gencode Version.
# \item \strong{genomeBuild.} Genome version.
# \item \strong{description.}
# }
apiRef_genes <- function(genes="", geneType="geneSymbol", gencodeVersion="v26", genomeBuild="GRCh38/hg38"){
# check null/na
if( is.null(genes) || any(is.na(genes)) || any(genes=="") ||length(genes)==0 ){
stop("Parameter \"genes\" can not be NULL or NA!")
}
# geneType
if( is.null(geneType) || any(is.na(geneType)) || any(geneType=="") || length(geneType)!=1){
stop("Parameter \"geneType\" should be choosen from \"geneSymbol\", \"gencodeId\", \"entrezId\".")
}else if( !(geneType %in% c("geneSymbol", "gencodeId", "entrezId","geneCategory")) ){
stop("Parameter \"geneType\" should be choosen from \"geneSymbol\", \"gencodeId\", \"entrezId\",\"geneCategory\".")
}
# gencodeVersion
if( is.null(gencodeVersion) || any(is.na(gencodeVersion)) || any(gencodeVersion=="") || length(gencodeVersion)!=1){
stop("Parameter \"gencodeVersion\" should be choosen from \"v26\", \"v19\".")
}else if( !(gencodeVersion %in% c("v26", "v19")) ){
stop("Parameter \"gencodeVersion\" should be choosen from \"v26\", \"v19\".")
}
# genomeBuild
# check gencodeVersion match with genomeBuild
if( is.null(genomeBuild) || any(is.na(genomeBuild)) || any(genomeBuild=="") || length(genomeBuild)!=1){
stop("Parameter \"genomeBuild\" should be choosen from \"GRCh38/hg38\", \"GRCh37/hg19\".")
}else if( !(genomeBuild %in% c("GRCh38/hg38", "GRCh37/hg19")) ){
stop("Parameter \"genomeBuild\" should be choosen from \"GRCh38/hg38\", \"GRCh37/hg19\".")
} else if(gencodeVersion=="v26" & genomeBuild=="GRCh38/hg38"){
# data(gencodeGeneInfoV26)
# gencodeGeneInfo <- data.table::copy(gencodeGeneInfoV26)
gencodeGeneInfo <- xQTLquery_geneAll("v26")
}else if(gencodeVersion=="v19" & genomeBuild=="GRCh37/hg19"){
# data(gencodeGeneInfoV19)
# gencodeGeneInfo <- data.table::copy(gencodeGeneInfoV19)
gencodeGeneInfo <- xQTLquery_geneAll("v19")
}else{
stop("gencodeVersion must be matched with genomeBuild.\n eg. v26(GRCh38/hg38), v19(GRCh37/hg19)")
}
# merge:
if( geneType=="geneSymbol" ){
genesDT <- data.table::data.table(genes=as.character(genes))
genesDT$geneSymbolUpper <- toupper(genesDT$genes)
gencodeGeneInfo$geneSymbolUpper<- toupper(gencodeGeneInfo$geneSymbol)
genesDTout <- merge(genesDT, gencodeGeneInfo, by ="geneSymbolUpper", sort=FALSE)
genesDTout <- genesDTout[,-c("geneSymbolUpper")]
if( nrow(genesDTout) >0){
if( length(genes)>1 ){
message("Queried ",length(genes), " genes, finally ",nrow(genesDTout)," records matched!")
}else if( length(genes)==1 ){
message("Queried ",length(genes), " gene, finally ",nrow(genesDTout)," record matched!")
}
return(genesDTout)
}else{
if( length(genes)>1 ){
message("Queried ",length(genes), " genes, finally 0 record matched!\nplease check your input genes!")
}else if( length(genes)==1 ){
message("Queried ",length(genes), " gene, finally 0 record matched!\nplease check your input genes!")
}
return(data.table::data.table(genes=genes))
}
}
# gencodeId
if( geneType=="gencodeId" ){
genesDT <- data.table::data.table(genes=as.character(genes))
genesDT$gencodeIdUpper <- toupper(genesDT$genes)
gencodeGeneInfo$gencodeIdUpper<- toupper(gencodeGeneInfo$gencodeId)
gencodeGeneInfo$gencodIdUv <- unlist(lapply(gencodeGeneInfo$gencodeId, function(x){ stringr::str_split_fixed(x, stringr::fixed("."),2)[1] }))
gencodeGeneInfo$gencodIdUvUpper<- toupper(gencodeGeneInfo$gencodIdUv)
genesDTout_1 <- merge(genesDT, gencodeGeneInfo, by ="gencodeIdUpper", sort=FALSE)
genesDTout_2 <- merge( gencodeGeneInfo, genesDT, by.y ="gencodeIdUpper", by.x= "gencodIdUvUpper", sort=FALSE)
genesDTout <- rbind(genesDTout_1, genesDTout_2)[,c("genes",names(gencodeGeneInfo[,-c("gencodeIdUpper", "gencodIdUv", "gencodIdUvUpper")])),with=FALSE]
if( nrow(genesDTout) >0){
message("Queried ",length(genes), " genes, finally ",nrow(genesDTout)," records matched!")
return(genesDTout)
}else{
message("Queried ",length(genes), " genes, finally 0 records matched!\nplease check your input genes!")
return(data.table::data.table(genes=genes))
}
# entrezId
}else if( geneType=="entrezId" ){
if( !all(unlist(lapply(genes, is.numeric))) ){
stop("Integer is requeried for entrezId!")
}
genesDT <- data.table::data.table(genes=genes)
gencodeGeneInfo$genes <- gencodeGeneInfo$entrezGeneId
genesDTout <- merge(genesDT, gencodeGeneInfo, by ="genes", sort=FALSE)
if( nrow(genesDTout) >0){
message("Queried ",length(genes), " genes, finally ",nrow(genesDTout)," records matched!")
return(genesDTout)
}else{
message("Queried ",length(genes), " genes, finally 0 records matched!\nplease check your input genes!")
return(data.table::data.table(genes=genes))
}
# geneCategory
}else if(geneType == "geneCategory"){
geneCategory = unique(gencodeGeneInfo$geneType)
if( length(genes)!=1 || any(!(genes %in% geneCategory)) ){
message(paste0(1:length(geneCategory),". ",geneCategory, collapse = "\n"))
stop("if \"geneType\" is \"geneCategory\", input \"genes\" should be choosen from the above: ")
}else{
genesDTout <- cbind(data.table(genes=gencodeGeneInfo[geneType==genes,]$geneSymbol), gencodeGeneInfo[geneType==genes,])
return(genesDTout)
}
}else{
return(data.table::data.table(genes=genes))
}
}
# @title Create gene annotation data
# @import data.table
# @import stringr
# @return NULL
createGencodeGeneInfoAll <- function(){
gencodeId <- chromosome <- strand <- gencodeId_unversioned <- startV26 <- startV19 <- NULL
.<-NULL
# # 生成 gencodeGeneInfoAllGranges
gencodeGeneInfoV26<- xQTLquery_geneAll("v26")
gencodeGeneInfoV19<- xQTLquery_geneAll("v19")
gencodeGeneInfoV26<- gencodeGeneInfoV26[,.(gencodeId, chromosome, start, end, strand, gencodeId_unversioned= unlist(lapply(gencodeId, function(x){str_split(x, fixed("."))[[1]][1]})))]
gencodeGeneInfoV19 <- gencodeGeneInfoV19[,.(gencodeId, chromosome=paste0("chr",chromosome), start, end, strand, gencodeId_unversioned =unlist(lapply(gencodeId, function(x){str_split(x, fixed("."))[[1]][1]})) )]
gencodeGeneInfoAll <- merge(gencodeGeneInfoV26[,.(gencodeId, gencodeId_unversioned, chromosome, strand, start, end)], gencodeGeneInfoV19[,.(gencodeId, gencodeId_unversioned, chromosome, strand, start, end)], by=c("gencodeId_unversioned", "chromosome", "strand"), all=TRUE, suffixes=c("V26","V19"))
gencodeGeneInfoAll <- gencodeGeneInfoAll[chromosome %in% paste0("chr",c(1:22,"X", "Y")),][order(chromosome, -startV26, -startV19)]
gencodeGeneInfoAllGranges <- GenomicRanges::GRanges(ifelse(is.na(gencodeGeneInfoAll$chromosome),"NA",gencodeGeneInfoAll$chromosome),
IRanges::IRanges(ifelse(is.na(gencodeGeneInfoAll$startV26),-1,gencodeGeneInfoAll$startV26), ifelse(is.na(gencodeGeneInfoAll$endV26),-1,gencodeGeneInfoAll$endV26)),
strand= ifelse(is.na(gencodeGeneInfoAll$strand),"*",gencodeGeneInfoAll$strand)
)
gencodeGeneInfoAllGranges$rangesV19 <- IRanges::IRanges(ifelse(is.na(gencodeGeneInfoAll$startV19),-1,gencodeGeneInfoAll$startV19), ifelse(is.na(gencodeGeneInfoAll$endV19),-1,gencodeGeneInfoAll$endV19))
gencodeGeneInfoAllGranges$gencodeId <- gencodeGeneInfoAll$gencodeId_unversioned
usethis::use_data(gencodeGeneInfoAllGranges, overwrite = TRUE)
# # usethis::use_data(gencodeGeneInfoAll, overwrite = TRUE)
return(NULL)
}
# httr::use_proxy(url="127.0.0.1", port=7890
# # ,username="dd",password="123456"
# )
# devtools::build("D:/R_project/GTExbiolinks","D:/R_project/GTExbiolinks.tar.gz")
#
# install.packages("~/GTExbiolinks.tar.gz", repos = NULL, type = "source")
# install.packages("~/GTExbiolinks.tar.gz", repos = NULL, type = "source", lib="/home/dingruofan/anaconda3/envs/work/lib/R/library")
# install.packages("~/GTExbiolinks_0.0.0.9000.tar.gz", repos = NULL, type = "source", lib="/home/dingruofan/anaconda3/envs/work/lib/R/library")
# import:
# usethis::use_package("data.table",min_version ="1.14.2")
# usethis::use_package("curl", min_version = "4.3.2")
# usethis::use_package("jsonlite", min_version = "1.7.2")
# usethis::use_package("stringr", min_version = "1.4.0")
# usethis::use_package("utils", min_version = "4.0.3")
# usethis::use_package("SummarizedExperiment", min_version = "1.18.2")
# usethis::use_package("ggplot2", min_version = "3.3.5")
# usethis::use_package("httr", min_version = "1.4.2")
# usethis::use_package("RMySQL", min_version = "0.10.22")
# usethis::use_package("DBI", min_version = "1.1.1") # in RMySQL
# usethis::use_package("PupillometryR", min_version = "0.0.4")
# usethis::use_package("ggpubr", min_version = "0.4.0")
# usethis::use_package("GenomeInfoDb", min_version = "1.24.2") # in GenomicRanges
# usethis::use_package("IRanges", min_version = "2.22.2") # in GenomicRanges
# usethis::use_package("ggrepel", min_version = "0.9.1") # in ggpubr
# usethis::use_package("coloc", min_version = "5.1.0")
# usethis::use_package("GenomicRanges", min_version = "1.40.0") # in SummarizedExperiment
# no version info:
# usethis::use_package("data.table",min_version ="1.14.2")
# usethis::use_package("curl", min_version = "4.3.2")
# usethis::use_package("jsonlite", min_version = "1.7.2")
# usethis::use_package("stringr", min_version = "1.4.0")
# usethis::use_package("utils", min_version = "4.0.3")
# usethis::use_package("SummarizedExperiment", min_version = "1.4.0")
# usethis::use_package("ggplot2", min_version="3.3.6")
# usethis::use_package("RMySQL")
# usethis::use_package("DBI") # in RMySQL
# usethis::use_package("ggridges")
# usethis::use_package("viridis")
# usethis::use_package("GenomeInfoDb") # in GenomicRanges
# usethis::use_package("IRanges") # in GenomicRanges
# usethis::use_package("ggrepel") # in ggpubr
# usethis::use_package("GenomicRanges") # in SummarizedExperiment
# usethis::use_package("BiocGenerics")
# usethis::use_package("cowplot", min_version="1.1.1")
# usethis::use_package("GenomicFeatures")
# usethis::use_package("VariantAnnotation")
# usethis::use_package("TxDb.Hsapiens.UCSC.hg38.knownGene")
# usethis::use_package("SummarizedExperiment")
#
# # suggest:
# usethis::use_package("usethis", type="Suggests")
# usethis::use_package("knitr", type="Suggests")
# usethis::use_package("rtracklayer",type="Suggests")
# usethis::use_package("coloc",type="Suggests")
# usethis::use_package("hyprcoloc",type="Suggests")
# usethis::use_package("PupillometryR")
# usethis::use_package("ggridges", type="Suggests")
# usethis::use_package("viridis", type="Suggests")
# usethis::use_package("crayon", min_version = "1.4.1") # message 字体：
# usethis::use_package("ggeextra", min_version = "1.4.1") # message 字体：
# usethis::use_package("rlang", min_version = "0.4.11", type="Suggests") # in ggpubr
# usethis::use_package("httr")
# usethis::use_package("scales")
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