'destdir' is ignored when GPL file is downloaded for local GSE matrix file

[biochem-fan]

When I try to load a (manually downloaded) GSE matrix file by

getGEO(filename="GSEXXXX_series_matrix.txt", destdir="./")

the destdir option is not passed to parseGSEMatrix() through parseGEO().
Therefore, GPL file is not searched in the destdir, but downloaded
into a temporary folder every time R is restarted.

[zhilongjia]

getGEO cannot use local GPL file directly when GPL is true so far due to a bug in function parseGSEMatrix. In this function, the parameter "destdir=tempdir()" should be "destdir=destdir", which should also be added into other related function parseGEO.

I suggest another parameter should be add. Two files will be reivsed (getGEO.R and parseGEO.R ) with a new parameter GPLfn.
It will look like

getGEO(filename="../GSE31747_series_matrix.txt.gz", GPLfn="../GPL8300.soft")

##################################################################
$git diff getGEO.R
diff --git a/R/getGEO.R b/R/getGEO.R
index 06bde57..912b23c 100644
--- a/R/getGEO.R
+++ b/R/getGEO.R
@@ -3,7 +3,8 @@ getGEO <- function(GEO=NULL,
destdir=tempdir(),
GSElimits=NULL,GSEMatrix=TRUE,
AnnotGPL=FALSE,

•               getGPL=TRUE) {
  

•               getGPL=TRUE,
  

•               GPLfn=NULL) {
  

  con <- NULL
  if(!is.null(GSElimits)) {
  if(length(GSElimits)!=2) {
  @@ -21,6 +22,6 @@ getGEO <- function(GEO=NULL,
  }
  filename <- getGEOfile(GEO,destdir=destdir,AnnotGPL=AnnotGPL)
  }
• ret <- parseGEO(filename,GSElimits)
• ret <- parseGEO(filename,GSElimits, GPLfn)
  return(ret)
  }
  ##################################################################

$git diff parseGEO.R

diff --git a/R/parseGEO.R b/R/parseGEO.R
index 813c996..c6b499f 100644
--- a/R/parseGEO.R
+++ b/R/parseGEO.R
@@ -1,4 +1,4 @@
-parseGEO <- function(fname,GSElimits) {
+parseGEO <- function(fname,GSElimits,GPLfn=NULL) {
con <- fileOpen(fname)
first.entity <- findFirstEntity(con)
close(con)
@@ -14,7 +14,7 @@ parseGEO <- function(fname,GSElimits) {
parseGPL(fname)
},
"0" = {

•                  parseGSEMatrix(fname)$eset
  

•                  parseGSEMatrix(fname, GPLfn=GPLfn)$eset
             },
             )
  

  return(ret)
  @@ -368,7 +368,7 @@ getAndParseGSEMatrices <- function(GEO,destdir,AnnotGPL,getGPL=TRUE) {

  Function to parse a single GSEMatrix

  file into an ExpressionSet

  -parseGSEMatrix <- function(fname,AnnotGPL=FALSE,destdir=tempdir(),getGPL=TRUE) {
  +parseGSEMatrix <- function(fname,AnnotGPL=FALSE,destdir=tempdir(),getGPL=TRUE, GPLfn=NULL) {
  dat <- readLines(fname)

  get the number of !Series and !Sample lines

  nseries <- sum(grepl("^!Series_", dat))
  @@ -406,7 +406,12 @@ parseGSEMatrix <- function(fname,AnnotGPL=FALSE,destdir=tempdir(),getGPL=TRUE) {

  if getGPL is FALSE, skip this and featureData is then a data.frame with no columns

  fd = new("AnnotatedDataFrame",data=data.frame(row.names=rownames(datamat)))
  if(getGPL) {

•    gpl <- getGEO(GPL,AnnotGPL=AnnotGPL,destdir=destdir)
  

•    if (!is.null(GPLfn)) {
  

•        gpl <- getGEO(filename=GPLfn, AnnotGPL=FALSE,destdir=destdir)
  

•    } else {
  

•        gpl <- getGEO(GEO=GPL,AnnotGPL=AnnotGPL,destdir=destdir)
  

•    }
  

•  vmd <- Columns(gpl)
   dat <- Table(gpl)
   ## GEO uses "TAG" instead of "ID" for SAGE GSE/GPL entries, but it is apparently
  

  ##################################################################