R/buildOwn.R
In guokai8/bioAnno: Build Annotation From Online Database
Defines functions
fromOwn
Documented in
fromOwn
#' build Own annotation database with user defined annotation file
#' @importFrom AnnotationForge makeOrgPackage
#' @importFrom utils install.packages
#' @importFrom stats na.omit
#' @importFrom stringr str_trim
#' @param geneinfo gene information table with two columns
#' as default("GID","DESCRIPTION")
#' @param keytype key type for building the annotation db
#' @param gene2go Gene Onotoly information for genes
#' @param gene2path KEGG Pathway information for genes
#' @param gene2symbol SYMBOL information for genes
#' @param gene2refseq REFSEQ or KO information for genes
#' @param gene2ensembl ENSEMBL or KO information for genes
#' @param gene2pfam PFAM information for genes
#' @param gene2reactome REACTOME Pathway or KO information for genes
#' @param gene2ko KO information for genes
#' @param gene2interpro INTERPRO information for genes
#' @param gene2entrezid ENTREZID information for genes
#' @param gene2biocyc BIOCYC information for genes
#' @param gene2kd KEGG DISEASE information for genes
#' @param gene2gad GAD information for genes
#' @param gene2fundo FunDO information for genes
#' @param author author for the annotation package
#' @param maintainer maintainer for the annotation package
#' @param tax_id taxonomy id for the species
#' @param genus genus for the species
#' @param version version for the annotation package
#' @param species species name(common name,kegg.species.code or scientifc name)
#' @param install install the package or not(default: TRUE)
#' @param pkgname package name you want to choose
#' @param outputDir temporary output path
#' @export
#' @examples
#' ## build your own annotation for Arabidopsis thaliana
#' data(ath)
#' fromOwn(geneinfo = ath, install = FALSE)
#' @return annotation package
#' @author Kai Guo
fromOwn <- function(geneinfo = geneinfo, keytype = NULL, gene2go = NULL, gene2path = NULL,
gene2symbol = NULL, gene2refseq = NULL, gene2ensembl = NULL,
gene2pfam = NULL, gene2reactome= NULL, gene2ko = NULL,
gene2interpro = NULL, gene2entrezid= NULL, gene2biocyc = NULL,
gene2kd = NULL,gene2fundo =NULL, gene2gad = NULL,
version = NULL, maintainer = NULL, author = NULL, outputDir = NULL,
tax_id = NULL, genus = NULL, species = NULL, install = TRUE, pkgname=NULL,rebuild=FALSE){
cat("Please make sure you have Gene Ontology and KEGG pathway
or KO data.frame ready.\n")
dbname1 <- paste0('org.', pkgname, '.eg.db')
if(isTRUE(rebuild)){
suppressMessages(remove.packages(dbname1))
}
if(is.null(geneinfo)){
stop("You must have Gene information table")
}
colnames(geneinfo)[1] <- "GID"
#1
geneinfo <- geneinfo[!duplicated(geneinfo), ]
geneinfo <- na.omit(geneinfo)
colnames(geneinfo)<-c('GID','GENENAME')
geneinfo$GID<-str_trim(geneinfo$GID,side = "both")
geneinfo$GENENAME<-str_trim(geneinfo$GENENAME,side = "both")
#2
if(!is.null(gene2go)){
if(ncol(gene2go) == 2){
gene2go$EVIDENCE <- "IEA"
colnames(gene2go)[c(1,2)] <- c("GID", "GO")
}else{
colnames(gene2go) <- c("GID", "GO", "EVIDENCE")
}
gene2go <- gene2go[!duplicated(gene2go), ]
gene2go <- na.omit(gene2go)
}else{
gene2go <- data.frame("GID" = geneinfo$GID,
"GO" = "GO:0008150", "EVIDENCE" = "IEA")
}
#3
if(!is.null(gene2path)){
if(ncol(gene2path) != 2){
stop("Dataframe must have only two columns")
}
colnames(gene2path) <- c("GID", "PATH")
gene2path <- gene2path[!duplicated(gene2path), ]
gene2path <- na.omit(gene2path)
}else{
gene2path <- data.frame("GID" = geneinfo$GID,
"PATH" = "")
}
#4
if(!is.null(gene2symbol)){
if(ncol(gene2symbol) != 2){
stop("Dataframe must have only two columns")
}
colnames(gene2symbol) <- c("GID", "SYMBOL")
gene2symbol <- gene2symbol[!duplicated(gene2symbol), ]
gene2symbol <- na.omit(gene2symbol)
}else if(keytype=="SYMBOL"){
gene2symbol <- data.frame("GID" = geneinfo$GID,
"SYMBOL" = geneinfo$GID)
}else{
gene2symbol <- data.frame("GID" = geneinfo$GID[1],
"SYMBOL" = "")
}
#5
if(!is.null(gene2ensembl)){
if(ncol(gene2ensembl) != 2){
stop("Dataframe must have only two columns")
}
colnames(gene2ensembl) <- c("GID", "ENSEMBL")
gene2ensembl <- gene2ensembl[!duplicated(gene2ensembl), ]
gene2ensembl <- na.omit(gene2ensembl)
}else if(keytype == "ENSEMBL"){
gene2ensembl <- data.frame("GID" = geneinfo$GID,
"ENSEMBL" = geneinfo$GID)
}else{
gene2ensembl <- data.frame("GID" = geneinfo$GID[1],
"ENSEMBL" = "")
}
#6
if(!is.null(gene2refseq)){
if(ncol(gene2refseq) != 2){
stop("Dataframe must have only two columns")
}
colnames(gene2refseq) <- c("GID", "REFSEQ")
gene2refseq <- gene2refseq[!duplicated(gene2refseq), ]
gene2refseq <- na.omit(gene2refseq)
}else if(keytype == "REFSEQ"){
gene2refseq <- data.frame("GID" = geneinfo$GID,
"REFSEQ" = geneinfo$GID)
}else{
gene2refseq <- data.frame("GID" = geneinfo$GID,
"REFSEQ" = "")
}
#7
if(!is.null(gene2pfam)){
if(ncol(gene2pfam) != 2){
stop("Dataframe must have only two columns")
}
colnames(gene2pfam) <- c("GID", "PFAM")
gene2pfam <- gene2pfam[!duplicated(gene2pfam), ]
gene2pfam <- na.omit(gene2pfam)
}else{
gene2pfam <- data.frame("GID" = geneinfo$GID[1],
"PFAM" = "")
}
#8
if(!is.null(gene2interpro)){
if(ncol(gene2interpro) != 2){
stop("Dataframe must have only two columns")
}
colnames(gene2interpro) <- c("GID", "INTERPRO")
gene2interpro <- gene2interpro[!duplicated(gene2interpro), ]
gene2interpro <- na.omit(gene2interpro)
}else{
gene2interpro <- data.frame("GID" = geneinfo$GID[1],
"INTERPRO" = "")
}
#9
if(!is.null(gene2reactome)){
if(ncol(gene2reactome) != 2){
stop("Dataframe must have only two columns")
}
colnames(gene2reactome) <- c("GID", "REACTOME")
gene2reactome <- gene2reactome[!duplicated(gene2reactome), ]
gene2reactome <- na.omit(gene2reactome)
}else{
gene2reactome <- data.frame("GID" = geneinfo$GID[1],
"REACTOME" = "")
}
#10
if(!is.null(gene2ko)){
if(ncol(gene2ko) != 2){
stop("Dataframe must have only two columns")
}
colnames(gene2ko) <- c("GID", "KO")
gene2ko <- gene2ko[!duplicated(gene2ko), ]
gene2ko <- na.omit(gene2ko)
}else{
gene2ko <- data.frame("GID" = geneinfo$GID[1],
"KO" = "")
}
#11
if(!is.null(gene2entrezid)){
if(ncol(gene2entrezid) != 2){
stop("Dataframe must have only two columns")
}
colnames(gene2entrezid) <- c("GID", "ENTREZID")
gene2entrezid <- gene2entrezid[!duplicated(gene2entrezid), ]
gene2entrezid <- na.omit(gene2entrezid)
}else if(keytype == "ENTREZID"){
gene2entrezid <- data.frame("GID" = geneinfo$GID,
"ENTREZID" = geneinfo$GID)
}else{
gene2entrezid <- data.frame("GID" = geneinfo$GID[1],
"ENTREZID" = "")
}
#12
if(!is.null(gene2biocyc)){
if(ncol(gene2biocyc) != 2){
stop("Dataframe must have only two columns")
}
colnames(gene2biocyc) <- c("GID", "BIOCYC")
gene2biocyc <- gene2biocyc[!duplicated(gene2biocyc), ]
gene2biocyc <- na.omit(gene2biocyc)
}else{
gene2biocyc <- data.frame("GID" = geneinfo$GID[1],
"BIOCYC" = "")
}
#13
if(!is.null(gene2kd)){
if(ncol(gene2kd) != 2){
stop("Dataframe must have only two columns")
}
colnames(gene2kd) <- c("GID", "KEGGDISEASE")
gene2kd <- gene2kd[!duplicated(gene2kd), ]
gene2kd <- na.omit(gene2kd)
}else{
gene2kd <- data.frame("GID" = geneinfo$GID[1],
"KEGGDISEASE" = "")
}
#14
if(!is.null(gene2gad)){
if(ncol(gene2gad) != 2){
stop("Dataframe must have only two columns")
}
colnames(gene2gad) <- c("GID", "GAD")
gene2gad <- gene2gad[!duplicated(gene2gad), ]
gene2gad <- na.omit(gene2gad)
}else{
gene2gad <- data.frame("GID" = geneinfo$GID[1],
"GAD" = "")
}
##
#15
if(!is.null(gene2fundo)){
if(ncol(gene2fundo) != 2){
stop("Dataframe must have only two columns")
}
colnames(gene2fundo) <- c("GID", "FUNDO")
gene2fundo <- gene2fundo[!duplicated(gene2fundo), ]
gene2fundo <- na.omit(gene2fundo)
}else{
gene2fundo <- data.frame("GID" = geneinfo$GID[1],
"FUNDO" = "")
}
##
if(is.null(version)){
version <- "0.0.1"
}
if(is.null(tax_id)){
tax_id <- "xxx"
}
if(is.null(author)){
author <- "myself"
}
if(is.null(maintainer)){
maintainer <- "myself<myself@email.com>"
}
if(is.null(genus)){
genus <- ""
}
if(is.null(species)){
species <- "species"
}
if(!is.null(pkgname)){
species <- pkgname
}
if(is.null(outputDir)){
outputDir <- tempdir()
}
package <- suppressWarnings(makeOrgPackage(
gene_info = geneinfo,
symbol = gene2symbol,
refseq = gene2refseq,
entrezid = gene2entrezid,
go = gene2go,
path = gene2path,
ko = gene2ko,
pfam = gene2pfam,
interpro = gene2interpro,
reactome = gene2reactome,
ensembl = gene2ensembl,
biocyc = gene2biocyc,
disease = gene2kd,
gad = gene2gad,
fundo = gene2fundo,
version = version,
maintainer = maintainer,
author = author,
outputDir = outputDir,
tax_id = tax_id,
genus = genus,
species = species,
goTable = "go"
))
if(isTRUE(install)){
install.packages(package, repos = NULL, type = "source")
unlink(package, recursive = TRUE)
}else{
.show.path(package)
.show.tables(package)
#return(package)
}
}
guokai8/bioAnno documentation built on May 8, 2023, 12:42 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions fromOwn
Documented in fromOwn
#' build Own annotation database with user defined annotation file
#' @importFrom AnnotationForge makeOrgPackage
#' @importFrom utils install.packages
#' @importFrom stats na.omit
#' @importFrom stringr str_trim
#' @param geneinfo gene information table with two columns
#' as default("GID","DESCRIPTION")
#' @param keytype key type for building the annotation db
#' @param gene2go Gene Onotoly information for genes
#' @param gene2path KEGG Pathway information for genes
#' @param gene2symbol SYMBOL information for genes
#' @param gene2refseq REFSEQ or KO information for genes
#' @param gene2ensembl ENSEMBL or KO information for genes
#' @param gene2pfam PFAM information for genes
#' @param gene2reactome REACTOME Pathway or KO information for genes
#' @param gene2ko KO information for genes
#' @param gene2interpro INTERPRO information for genes
#' @param gene2entrezid ENTREZID information for genes
#' @param gene2biocyc BIOCYC information for genes
#' @param gene2kd KEGG DISEASE information for genes
#' @param gene2gad GAD information for genes
#' @param gene2fundo FunDO information for genes
#' @param author author for the annotation package
#' @param maintainer maintainer for the annotation package
#' @param tax_id taxonomy id for the species
#' @param genus genus for the species
#' @param version version for the annotation package
#' @param species species name(common name,kegg.species.code or scientifc name)
#' @param install install the package or not(default: TRUE)
#' @param pkgname package name you want to choose
#' @param outputDir temporary output path
#' @export
#' @examples
#' ## build your own annotation for Arabidopsis thaliana
#' data(ath)
#' fromOwn(geneinfo = ath, install = FALSE)
#' @return annotation package
#' @author Kai Guo
fromOwn <- function(geneinfo = geneinfo, keytype = NULL, gene2go = NULL, gene2path = NULL,
gene2symbol = NULL, gene2refseq = NULL, gene2ensembl = NULL,
gene2pfam = NULL, gene2reactome= NULL, gene2ko = NULL,
gene2interpro = NULL, gene2entrezid= NULL, gene2biocyc = NULL,
gene2kd = NULL,gene2fundo =NULL, gene2gad = NULL,
version = NULL, maintainer = NULL, author = NULL, outputDir = NULL,
tax_id = NULL, genus = NULL, species = NULL, install = TRUE, pkgname=NULL,rebuild=FALSE){
cat("Please make sure you have Gene Ontology and KEGG pathway
or KO data.frame ready.\n")
dbname1 <- paste0('org.', pkgname, '.eg.db')
if(isTRUE(rebuild)){
suppressMessages(remove.packages(dbname1))
}
if(is.null(geneinfo)){
stop("You must have Gene information table")
}
colnames(geneinfo)[1] <- "GID"
#1
geneinfo <- geneinfo[!duplicated(geneinfo), ]
geneinfo <- na.omit(geneinfo)
colnames(geneinfo)<-c('GID','GENENAME')
geneinfo$GID<-str_trim(geneinfo$GID,side = "both")
geneinfo$GENENAME<-str_trim(geneinfo$GENENAME,side = "both")
#2
if(!is.null(gene2go)){
if(ncol(gene2go) == 2){
gene2go$EVIDENCE <- "IEA"
colnames(gene2go)[c(1,2)] <- c("GID", "GO")
}else{
colnames(gene2go) <- c("GID", "GO", "EVIDENCE")
}
gene2go <- gene2go[!duplicated(gene2go), ]
gene2go <- na.omit(gene2go)
}else{
gene2go <- data.frame("GID" = geneinfo$GID,
"GO" = "GO:0008150", "EVIDENCE" = "IEA")
}
#3
if(!is.null(gene2path)){
if(ncol(gene2path) != 2){
stop("Dataframe must have only two columns")
}
colnames(gene2path) <- c("GID", "PATH")
gene2path <- gene2path[!duplicated(gene2path), ]
gene2path <- na.omit(gene2path)
}else{
gene2path <- data.frame("GID" = geneinfo$GID,
"PATH" = "")
}
#4
if(!is.null(gene2symbol)){
if(ncol(gene2symbol) != 2){
stop("Dataframe must have only two columns")
}
colnames(gene2symbol) <- c("GID", "SYMBOL")
gene2symbol <- gene2symbol[!duplicated(gene2symbol), ]
gene2symbol <- na.omit(gene2symbol)
}else if(keytype=="SYMBOL"){
gene2symbol <- data.frame("GID" = geneinfo$GID,
"SYMBOL" = geneinfo$GID)
}else{
gene2symbol <- data.frame("GID" = geneinfo$GID[1],
"SYMBOL" = "")
}
#5
if(!is.null(gene2ensembl)){
if(ncol(gene2ensembl) != 2){
stop("Dataframe must have only two columns")
}
colnames(gene2ensembl) <- c("GID", "ENSEMBL")
gene2ensembl <- gene2ensembl[!duplicated(gene2ensembl), ]
gene2ensembl <- na.omit(gene2ensembl)
}else if(keytype == "ENSEMBL"){
gene2ensembl <- data.frame("GID" = geneinfo$GID,
"ENSEMBL" = geneinfo$GID)
}else{
gene2ensembl <- data.frame("GID" = geneinfo$GID[1],
"ENSEMBL" = "")
}
#6
if(!is.null(gene2refseq)){
if(ncol(gene2refseq) != 2){
stop("Dataframe must have only two columns")
}
colnames(gene2refseq) <- c("GID", "REFSEQ")
gene2refseq <- gene2refseq[!duplicated(gene2refseq), ]
gene2refseq <- na.omit(gene2refseq)
}else if(keytype == "REFSEQ"){
gene2refseq <- data.frame("GID" = geneinfo$GID,
"REFSEQ" = geneinfo$GID)
}else{
gene2refseq <- data.frame("GID" = geneinfo$GID,
"REFSEQ" = "")
}
#7
if(!is.null(gene2pfam)){
if(ncol(gene2pfam) != 2){
stop("Dataframe must have only two columns")
}
colnames(gene2pfam) <- c("GID", "PFAM")
gene2pfam <- gene2pfam[!duplicated(gene2pfam), ]
gene2pfam <- na.omit(gene2pfam)
}else{
gene2pfam <- data.frame("GID" = geneinfo$GID[1],
"PFAM" = "")
}
#8
if(!is.null(gene2interpro)){
if(ncol(gene2interpro) != 2){
stop("Dataframe must have only two columns")
}
colnames(gene2interpro) <- c("GID", "INTERPRO")
gene2interpro <- gene2interpro[!duplicated(gene2interpro), ]
gene2interpro <- na.omit(gene2interpro)
}else{
gene2interpro <- data.frame("GID" = geneinfo$GID[1],
"INTERPRO" = "")
}
#9
if(!is.null(gene2reactome)){
if(ncol(gene2reactome) != 2){
stop("Dataframe must have only two columns")
}
colnames(gene2reactome) <- c("GID", "REACTOME")
gene2reactome <- gene2reactome[!duplicated(gene2reactome), ]
gene2reactome <- na.omit(gene2reactome)
}else{
gene2reactome <- data.frame("GID" = geneinfo$GID[1],
"REACTOME" = "")
}
#10
if(!is.null(gene2ko)){
if(ncol(gene2ko) != 2){
stop("Dataframe must have only two columns")
}
colnames(gene2ko) <- c("GID", "KO")
gene2ko <- gene2ko[!duplicated(gene2ko), ]
gene2ko <- na.omit(gene2ko)
}else{
gene2ko <- data.frame("GID" = geneinfo$GID[1],
"KO" = "")
}
#11
if(!is.null(gene2entrezid)){
if(ncol(gene2entrezid) != 2){
stop("Dataframe must have only two columns")
}
colnames(gene2entrezid) <- c("GID", "ENTREZID")
gene2entrezid <- gene2entrezid[!duplicated(gene2entrezid), ]
gene2entrezid <- na.omit(gene2entrezid)
}else if(keytype == "ENTREZID"){
gene2entrezid <- data.frame("GID" = geneinfo$GID,
"ENTREZID" = geneinfo$GID)
}else{
gene2entrezid <- data.frame("GID" = geneinfo$GID[1],
"ENTREZID" = "")
}
#12
if(!is.null(gene2biocyc)){
if(ncol(gene2biocyc) != 2){
stop("Dataframe must have only two columns")
}
colnames(gene2biocyc) <- c("GID", "BIOCYC")
gene2biocyc <- gene2biocyc[!duplicated(gene2biocyc), ]
gene2biocyc <- na.omit(gene2biocyc)
}else{
gene2biocyc <- data.frame("GID" = geneinfo$GID[1],
"BIOCYC" = "")
}
#13
if(!is.null(gene2kd)){
if(ncol(gene2kd) != 2){
stop("Dataframe must have only two columns")
}
colnames(gene2kd) <- c("GID", "KEGGDISEASE")
gene2kd <- gene2kd[!duplicated(gene2kd), ]
gene2kd <- na.omit(gene2kd)
}else{
gene2kd <- data.frame("GID" = geneinfo$GID[1],
"KEGGDISEASE" = "")
}
#14
if(!is.null(gene2gad)){
if(ncol(gene2gad) != 2){
stop("Dataframe must have only two columns")
}
colnames(gene2gad) <- c("GID", "GAD")
gene2gad <- gene2gad[!duplicated(gene2gad), ]
gene2gad <- na.omit(gene2gad)
}else{
gene2gad <- data.frame("GID" = geneinfo$GID[1],
"GAD" = "")
}
##
#15
if(!is.null(gene2fundo)){
if(ncol(gene2fundo) != 2){
stop("Dataframe must have only two columns")
}
colnames(gene2fundo) <- c("GID", "FUNDO")
gene2fundo <- gene2fundo[!duplicated(gene2fundo), ]
gene2fundo <- na.omit(gene2fundo)
}else{
gene2fundo <- data.frame("GID" = geneinfo$GID[1],
"FUNDO" = "")
}
##
if(is.null(version)){
version <- "0.0.1"
}
if(is.null(tax_id)){
tax_id <- "xxx"
}
if(is.null(author)){
author <- "myself"
}
if(is.null(maintainer)){
maintainer <- "myself<myself@email.com>"
}
if(is.null(genus)){
genus <- ""
}
if(is.null(species)){
species <- "species"
}
if(!is.null(pkgname)){
species <- pkgname
}
if(is.null(outputDir)){
outputDir <- tempdir()
}
package <- suppressWarnings(makeOrgPackage(
gene_info = geneinfo,
symbol = gene2symbol,
refseq = gene2refseq,
entrezid = gene2entrezid,
go = gene2go,
path = gene2path,
ko = gene2ko,
pfam = gene2pfam,
interpro = gene2interpro,
reactome = gene2reactome,
ensembl = gene2ensembl,
biocyc = gene2biocyc,
disease = gene2kd,
gad = gene2gad,
fundo = gene2fundo,
version = version,
maintainer = maintainer,
author = author,
outputDir = outputDir,
tax_id = tax_id,
genus = genus,
species = species,
goTable = "go"
))
if(isTRUE(install)){
install.packages(package, repos = NULL, type = "source")
unlink(package, recursive = TRUE)
}else{
.show.path(package)
.show.tables(package)
#return(package)
}
}
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