To obtain metadata from GSM**** files

extractMetaGsm.R

library(GEOquery)


extractMetaGsm <- function(GEO){
	require(GEOquery)
	GSElimits=NULL
	AnnotGPL=FALSE
	destdir <- tempdir()
	meta <- list()
	for (i in 1:length(GEO)){
		filename <- my.getGEOfile(GEO[i],destdir=destdir,AnnotGPL=AnnotGPL)
		txt <- read.csv(filename, nrow=100)[1:100,1]
		meta[[i]] <- GEOquery:::parseGeoMeta(txt)
		cat(i)
		cat("\n")
	}
	meta
}

my.getGEOfile <- function(GEO,destdir=tempdir(),AnnotGPL=FALSE,
                       amount=c('full','brief','quick','data'))
  {
    amount <- match.arg(amount)
    geotype <- toupper(substr(GEO,1,3))
    mode <- 'wb'
    GEO <- toupper(GEO)
    stub = gsub('\\d{1,3}$','nnn',GEO,perl=TRUE)
    if (geotype == 'GDS') {
      gdsurl <- 'ftp://ftp.ncbi.nlm.nih.gov/geo/datasets/%s/%s/soft/%s'
      myurl <- sprintf(gdsurl,stub,GEO,paste0(GEO,'.soft.gz'))
      destfile <- file.path(destdir,paste0(GEO,'.soft.gz'))
    }
    if (geotype == 'GSE' & amount=='full') {
      gseurl <- 'ftp://ftp.ncbi.nlm.nih.gov/geo/series/%s/%s/soft/%s'
      myurl <- sprintf(gseurl,stub,GEO,paste0(GEO,'_family.soft.gz'))
      destfile <- file.path(destdir,paste(GEO,'.soft.gz',sep=""))
    }
    if (geotype == 'GSE' & amount!='full' & amount!='table') {
      gseurl <- "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi"
      myurl <- paste(gseurl,'?targ=self&acc=',GEO,'&form=text&view=',amount,sep='')
      destfile <- file.path(destdir,paste(GEO,'.soft',sep=""))
      mode <- 'w'
    }
    
    if (geotype == 'GSM') {
      gseurl <- "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi"
      myurl <- paste(gseurl,'?targ=self&acc=',GEO,'&form=text&view=',amount,sep='')
      destfile <- file.path(destdir,paste(GEO,'.soft',sep=""))
      mode <- 'w'
    }
    if(!file.exists(destfile)) {
      download.file(myurl,destfile,mode=mode,quiet=TRUE,method=getOption('download.file.method.GEOquery'))
     }
    invisible(destfile)
  }