R/refreshData.R

In jmzeng1314/humanid: gene id annotation

#' extract probeset ID and entrez gene id from R packages
#'
#' So far, we just extract data from R packages:hgu95av2/hgu133a/hgu133b/hgu133plus2
#'
#' @param refresh Don't use this function if not neccessary
#' @keywords refresh

refreshMicroarrayData <- function(refresh = F) {
    if (refresh) {
        library(hgu95av2.db)
        library(hgu133a.db)
        library(hgu133b.db)
        library(hgu133plus2.db)

        hgu95av2_id <- toTable(hgu95av2ENTREZID)
        hgu133a_id <- toTable(hgu133aENTREZID)
        hgu133b_id <- toTable(hgu133bENTREZID)
        hgu133plus2_id <- toTable(hgu133plus2ENTREZID)

        # save(hgu95av2_id,hgu133a_id,hgu133b_id,hgu133plus2_id,file = 'probeset.Rdata')
        devtools::use_data(hgu95av2_id, hgu133a_id, hgu133b_id, hgu133plus2_id, overwrite = T)
    }


    # hgu95av2_id[ match(c(probeList),hgu95av2_id$probe_id),]
}

refreshGPL <- function(refresh = F) {
  if (refresh) {
    library(GEOmetadb)
    db='/Users/jmzeng/data/project/IDmap/GEOmetadb.sqlite'
    if(!file.exists(db)) getSQLiteFile()
    file.info(db)
    conGEO <- dbConnect(SQLite(),db)
    dbListTables(conGEO)
    dbListFields(conGEO,"gpl")
    gpl= dbGetQuery(conGEO,"select * from gpl ")
    r_gpl=gpl[!is.na(gpl$bioc_package),c(2,3,20)]
    # save(r_gpl,file = 'gpl_with_Rpackage.Rdata')

    devtools::use_data( r_gpl, overwrite = T)
  }


  # hgu95av2_id[ match(c(probeList),hgu95av2_id$probe_id),]
}


#' extract gene IDs from org.Hs.eg.db
#'
#' So far, we just extract gene entrez ID,ensembl ID,HUGO symbol,and locus.
#'
#' @param refresh Don't use this function if not neccessary
#' @keywords refresh

refreshOrgHsData <- function(refresh = F) {
    if (refresh) {
        library(org.Hs.eg.db)
        all_EG = mappedkeys(org.Hs.egSYMBOL)
        allSymbols = mappedkeys(org.Hs.egSYMBOL2EG)
        EG2Symbol = toTable(org.Hs.egSYMBOL)
        EG2name = toTable(org.Hs.egGENENAME)
        EG2MAP = toTable(org.Hs.egMAP)
        EG2ENSEMBL = toTable(org.Hs.egENSEMBL)
        EG2accnum = toTable(org.Hs.egREFSEQ)
        devtools::use_data(all_EG, allSymbols, EG2Symbol, EG2name, EG2MAP, EG2ENSEMBL, EG2accnum, overwrite = T)
    }
}

#' update kegg data
#'
#' It's not a automately function, please don't run it. it will read the files ind data folder, which is 'kegg2geneID.txt' and 'kegg_hierarchical.txt'
#' you must make sure the files exists in the data/KEGG_update folder.
#' It will process the files and store the GeneID2kegg_list,kegg2GeneID_list,keggID2geneID_df,kegg2name to the Rdata.
#' GeneID2kegg_list and kegg2GeneID_list are list which one key has multiple values.
#' keggID2geneID_df is a data.frame , 2 columns : 'gene_id','path_id'
#' kegg2name is a data.frame, which has 4 columns, which is :parent1 parent2 pathway_id pathway_name
#'
#' @param refresh Don't use this function if not neccessary
#' @keywords refresh

update_kegg <- function(refresh = F) {
    if (refresh) {
        dir_bin = "data"
        path2gene_file = file.path(dir_bin, "KEGG_update", "kegg2geneID.txt")
        path2name_file = file.path(dir_bin, "KEGG_update", "kegg_hierarchical.txt")
        if (file.exists(path2gene_file)) {
            keggID2geneID = read.table(path2gene_file, sep = "\t", colClasses = c("character"))
            keggID2geneID_df = keggID2geneID[, c(2, 1)]
            names(keggID2geneID_df) = c("gene_id", "path_id")
            tmp = read.table(path2gene_file, sep = "\t", colClasses = c("character"))
            # tmp=toTable(org.Hs.egPATH) first column is kegg ID, second column is entrez ID
            GeneID2kegg_list <<- tapply(tmp[, 1], as.factor(tmp[, 2]), function(x) x)
            kegg2GeneID_list <<- tapply(tmp[, 2], as.factor(tmp[, 1]), function(x) x)
        } else {
            stop("we can not find the file:path2gene_file")
        }
        if (file.exists(path2name_file)) {
            kegg2name <<- read.delim(path2name_file, header = F, sep = "\t", colClasses = c("character"), stringsAsFactors = F)
            colnames(kegg2name) = c("parent1", "parent2", "pathway_id", "pathway_name")
            ### kegg2name$pathway_id=as.numeric(kegg2name$pathway_id)
            rownames(kegg2name) = kegg2name$pathway_id
        } else {
            stop("we can not find the file:path2name_file")
        }

        devtools::use_data(keggID2geneID_df, GeneID2kegg_list, kegg2GeneID_list, kegg2name, overwrite = T)
    }
}

#' create the duplicated expression matrix
#'
#' the expression matrix come from the data 'sCLLex' in R package 'CLL'
#' duplicated because one gene symbol corresponding to multiple probeset ID in hgu95av2.db
#' dup_exprSet is a data.frame,  the first column is gene symbol, which needed to remove duplicated.
#'
#' @param refresh Don't use this function if not neccessary
#' @keywords refresh
#'
create_dup_exprSet <- function(refresh = F) {
    library(CLL)
    data(sCLLex)
    group_list = sCLLex$Disease

    library(annotate)
    exprSet = exprs(sCLLex)
    platformDB = "hgu95av2.db"
    library(platformDB, character.only = TRUE)
    probeset <- featureNames(sCLLex)
    SYMBOL <- lookUp(probeset, platformDB, "SYMBOL")
    dup_exprSet = cbind(SYMBOL, exprSet)

    devtools::use_data(dup_exprSet, overwrite = T)
}

#' create expression matrix,rowname are unique genes, colname are samples
#'
#' example_exprSet comes from rmDupID(dup_exprSet),also the data 'sCLLex' in R package 'CLL'
#'
#' @param refresh Don't use this function if not neccessary
#' @keywords refresh
#'
create_example_exprSet <- function(refresh = F) {
    example_exprSet = rmDupID(dup_exprSet)
    devtools::use_data(example_exprSet, overwrite = T)
}


#' create a list of gene sets for  enzyme/protein complex/ development/immune
#'
#' PTM: Post-translational modification, such methyl-,  acethyl-,  phospha-
#' SWI/SNF Chromatin Remodeling Complexes and PRC family members
#' development associated genes
#' Immune-Related Genes
#' transcription factor genesets
#' other genesets
#'
#' @param refresh Don't use this function if not neccessary
#' @keywords refresh
#'
create_genesets_list <- function(refresh = F) {

    suppressMessages(library("org.Hs.eg.db"))
    allSymbols = mappedkeys(org.Hs.egSYMBOL2EG)
    PRMT_list = allSymbols[grepl("^PRMT", allSymbols)]
    PRMT_list = c(PRMT_list, "CARM1")
    JMJD_list = allSymbols[grepl("^JMJD", allSymbols)]
    KMT_list = allSymbols[grepl("^KMT", allSymbols)]
    KMT_list = c(KMT_list, "EZH2")
    KDM_list = allSymbols[grepl("^KDM", allSymbols)]
    HAT_list = allSymbols[grepl("^KAT\\d", allSymbols)]
    HAT_list = c(HAT_list, "HAT1", "EP300")
    HDAC_list = allSymbols[grepl("^HDAC", allSymbols)]
    MAPK_list = allSymbols[grepl("^MAPK", allSymbols)]
    CDK_list = allSymbols[grepl("^CDK\\d+$", perl = T, allSymbols)]
    PRAK_list = allSymbols[grepl("^PRKA", perl = T, allSymbols)]
    DUSP_list = allSymbols[grepl("^DUSP\\d+$", allSymbols)]

    enzyme_genesets = list(PRMT_list, JMJD_list, KMT_list, KDM_list, HAT_list, HDAC_list, MAPK_list, CDK_list, PRAK_list,
        DUSP_list)
    names(enzyme_genesets) = strsplit("PRMT_list,JMJD_list,KMT_list,KDM_list,HAT_list,HDAC_list,MAPK_list,CDK_list,PRAK_list,DUSP_list",
        ",")[[1]]

    HIST_list = allSymbols[grepl("^HIST", allSymbols)]
    ABC_list = allSymbols[grepl("^ABC", allSymbols)]
    TUB_list = allSymbols[grepl("^TUB", allSymbols)]
    ACT_list = allSymbols[grepl("^ACT", allSymbols)]
    MYO_list = allSymbols[grepl("^MYO", allSymbols)]
    other_genesets = list(HIST_list, ABC_list, TUB_list, ACT_list, MYO_list)
    names(other_genesets) = strsplit("HIST_list,ABC_list,TUB_list,ACT_list,MYO_list", ",")[[1]]


    PRC_list = c("BMI1", "CBX2", "CBX4", "CBX7", "CBX8", "PCGF1", "PCGF2", "PCGF3", "PCGF5", "PCGF6", "PHC1", "PHC2",
        "PHC3", "RING1", "RNF2", "SCML1", "SCML2", "AEBP2", "EED", "EZH2", "HOXTAIR", "JARID2", "RBBP4", "RBBP6",
        "SUZ12", "GAPDH")
    SWI_SNF_list = allSymbols[grepl("^SMAR", allSymbols)]
    RNA_Polymerase_II_list = allSymbols[grepl("^POLR", allSymbols)]
    TAF_list = allSymbols[grepl("^TAF", allSymbols)]
    TBP_list = allSymbols[grepl("^TBP", allSymbols)]
    TATA_Box_TF_list = c(TAF_list, TBP_list)
    General_TF_list = allSymbols[grepl("^GTF", allSymbols)]
    nulear_Factor_list = allSymbols[grepl("^NF", allSymbols)]
    protein_complex_genesets = list(PRC_list, SWI_SNF_list, RNA_Polymerase_II_list, TATA_Box_TF_list, General_TF_list,
        nulear_Factor_list)
    names(protein_complex_genesets) = strsplit("PRC_list,SWI_SNF_list,RNA_Polymerase_II_list,TATA_Box_TF_list,General_TF_list,nulear_Factor_list",
        ",")[[1]]


    devtools::use_data(protein_complex_genesets, enzyme_genesets, other_genesets, overwrite = T)

}