R/ebi.R

In htc502/ewrefxn: this package collects r fxns useful in my daily coding life

#' fetch gene expression data from EBI arrayexpress
#'
#' this is a wrapper function which is used to download data from EBI arrayexpress
#' @param accession Accession number of the data, like 'E-GEOD-6039' etc
#' @param path the directory where downloaded files will be stored in
#' @param type be one of raw/processed/full; for download the raw/processed/both data
#' @param extract default to T, otherwise the downloaded data will not be extracted
#' @param local local files to be read instead of downloading from the server
#' @param sourcedir if local is TRUE, files will be read from this dir
#' @return return
#' @export
ebi.fetch <- function(accession, path = getwd(), type = 'full',
                      extract = T, local = F, sourcedir = path, ...) {
    if(!require0('ArrayExpress'))
        stop("error loading arrayexpress package\n")
    ##arrayexpress file name list returned
    ae.flist <- getAE(accession, path = getwd(), type = 'full',
                      extract = extract, local = local, sourcedir = sourcedir, ...)
    ae.flist
}
#' function to process agilent44k chip data
#' this function is part of the pipeline, the input is the value returned by ebi.fetch
#' @param ae.flist object returned by ebi.fetch fxn
#' @export
ebi.agilent44k.prep <- function( ae.flist ) {
    if(!("sdrf" %in% names(ae.flist)) )
        stop("sample&data relationship file(sdrf file) not found\n")
    SDRF <- read.delim(ae.flist$sdrf, stringsAsFactors = F,
                       check.names = F)
    cat("array data files we will process are shown bellow, to remove/add samples, manually edit the sdrf file...\n")
    print(SDRF[ ,"Array Data File" ])
#    answer <- dual.choice("sure we go ahead?",value1 = "y",value2="n")
#    if(answer == "n")
#        return(NULL)
    prep.obj <- agilent44k.prep(array.fnames = SDRF[ ,"Array Data File" ])
    prep.obj
}
#' function to process agilent80k chip data
#' this function actually calls ebi.agilent44k
#' @param ae.flist object returned by ebi.fetch fxn
#' @export
ebi.agilent80k.prep <- function(ae.flist) {
    res <- ebi.agilent44k.prep(ae.flist)
    res
}
#' preprocessing affymetrix chip data
#' @param ae.flist object returned by ebi.fetch
#' @export
ebi.affy.st.prep <- function(ae.flist) {
    if(!("sdrf" %in% names(ae.flist)) )
        stop("sample&data relationship file(sdrf file) not found\n")
    SDRF <- read.delim(ae.flist$sdrf, stringsAsFactors = F,
                       check.names = F)
    cat("array data files we will process are shown bellow, to remove/add samples, manually edit the sdrf file...\n")
    print(SDRF[ ,"Array Data File" ])
#    answer <- dual.choice("sure we go ahead?",value1 = "y",value2="n")
#    if(answer == "n")
#        return(NULL)
    prep.obj <- affy.st.prep(array.fnames = SDRF[ ,"Array Data File" ])
    prep.obj

}
#' function to processing affymetrix ivt chip data(exon chip)
#' @param ae.flist is the object returned by ebi.fetch
#' @export
ebi.affy.ivt.prep <- function(ae.flist) {
    if(!("sdrf" %in% names(ae.flist)) )
        stop("sample&data relationship file(sdrf file) not found\n")
    SDRF <- read.delim(ae.flist$sdrf, stringsAsFactors = F,
                       check.names = F)
    cat("array data files we will process are shown bellow, to remove/add samples, manually edit the sdrf file...\n")
    print(SDRF[ ,"Array Data File" ])
#    answer <- dual.choice("sure we go ahead?",value1 = "y",value2="n")
#    if(answer == "n")
#        return(NULL)
    prep.obj <- affy.ivt.prep(array.fnames = SDRF[ ,"Array Data File" ])
    prep.obj
}