bio-affy 0.1.0.alpha.1 → 0.5.0

data/README.rdoc

@@ -25,6 +25,22 @@ Next run the tool with
 
   bio-affy --help
 
+This module was written with 
+
+  ruby 1.9.3p0 (2011-10-30 revision 33570) [x86_64-linux]
+  Using rake (0.9.2.2) 
+  Using bundler (1.0.21) 
+  Using diff-lcs (1.1.3) 
+  Using ffi (1.0.11) 
+  Using git (1.2.5) 
+  Using jeweler (1.6.4) 
+  Using mkrf (0.2.3) 
+  Using rcov (0.9.11) 
+  Using rspec-core (2.7.1) 
+  Using rspec-expectations (2.7.0) 
+  Using rspec-mocks (2.7.0) 
+  Using rspec (2.7.0) 
+
 == Copyright
 
 Copyright (C) 2011 Pjotr Prins <pjotr.prins@thebird.nl> 

data/Rakefile

@@ -27,6 +27,7 @@ Jeweler::Tasks.new do |gem|
   gem.authors = ["Pjotr Prins"]
   gem.extensions = "ext/src/mkrf_conf.rb"
   gem.files += Dir['lib/**/*'] + Dir['ext/**/*']
+  gem.files.reject! { | n | n =~ /\.(o|so|gz|CDF|R|Rd|log)$/ }
   gem.rubyforge_project = "nowarning"
 
   # dependencies defined in Gemfile

data/VERSION

@@ -1 +1 @@
-0.1.0.alpha.1
+0.5.0

data/bio-affy.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "bio-affy"
-  s.version = "0.1.0.alpha.1"
+  s.version = "0.5.0"
 
-  s.required_rubygems_version = Gem::Requirement.new("> 1.3.1") if s.respond_to? :required_rubygems_version=
+  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Pjotr Prins"]
-  s.date = "2011-12-03"
+  s.date = "2011-12-05"
   s.description = "Affymetrix microarray file format parser\n  (CEL/CDF) for Ruby. FFI binding to Biolib port of R/Affyio by Benjamin Milo Bolstad"
   s.email = "pjotr.public01@thebird.nl"
   s.executables = ["bio-affy"]
@@ -33,63 +33,40 @@ Gem::Specification.new do |s|
     "ext/HISTORY",
     "ext/LICENSE",
     "ext/NAMESPACE",
-    "ext/R/check.cdf.type.R",
-    "ext/R/read.cdffile.list.R",
-    "ext/R/read.celfile.R",
-    "ext/R/read.celfile.header.R",
-    "ext/R/read.probematrices.R",
     "ext/README_BIOLIB",
     "ext/aclocal.m4",
     "ext/configure",
     "ext/configure.in",
-    "ext/man/check.cdf.type.Rd",
-    "ext/man/read.cdffile.list.Rd",
-    "ext/man/read.celfile.Rd",
-    "ext/man/read.celfile.header.Rd",
-    "ext/man/read.celfile.probeintensity.matrices.Rd",
     "ext/src/CMakeLists.txt",
     "ext/src/Makevars.in",
     "ext/src/Makevars.win",
     "ext/src/Rakefile",
+    "ext/src/biolib_R_map.c",
+    "ext/src/biolib_R_map.h",
     "ext/src/biolib_affyio.c",
     "ext/src/biolib_affyio.h",
-    "ext/src/biolib_affyio.o",
+    "ext/src/biolib_error.c",
+    "ext/src/biolib_error.h",
     "ext/src/fread_functions.c",
     "ext/src/fread_functions.h",
-    "ext/src/fread_functions.o",
-    "ext/src/libaffyext.so",
-    "ext/src/mkrf.log",
     "ext/src/mkrf_conf.rb",
     "ext/src/read_abatch.c",
     "ext/src/read_abatch.h",
-    "ext/src/read_abatch.o",
     "ext/src/read_bpmap.c",
-    "ext/src/read_bpmap.o",
     "ext/src/read_cdf.h",
     "ext/src/read_cdf_xda.c",
-    "ext/src/read_cdf_xda.o",
     "ext/src/read_cdffile2.c",
-    "ext/src/read_cdffile2.o",
     "ext/src/read_celfile_generic.c",
     "ext/src/read_celfile_generic.h",
-    "ext/src/read_celfile_generic.o",
     "ext/src/read_clf.c",
-    "ext/src/read_clf.o",
     "ext/src/read_generic.c",
     "ext/src/read_generic.h",
-    "ext/src/read_generic.o",
     "ext/src/read_pgf.c",
-    "ext/src/read_pgf.o",
     "lib/bio-affy.rb",
     "lib/bio/affy.rb",
     "lib/bio/affyext.rb",
-    "lib/bio/libaffyext.so",
     "spec/bio-affy_spec.rb",
-    "spec/spec_helper.rb",
-    "test/data/affy/GSM103328.CEL.gz",
-    "test/data/affy/GSM103329.CEL.gz",
-    "test/data/affy/GSM103330.CEL.gz",
-    "test/data/affy/MG_U74Av2.CDF.gz"
+    "spec/spec_helper.rb"
   ]
   s.homepage = "http://github.com/pjotrp/bioruby-affy"
   s.licenses = ["MIT"]

data/ext/src/Rakefile

@@ -18,7 +18,7 @@ INCLUDES = "-I/home/wrk/.rvm/rubies/ruby-1.9.3-p0/include/ruby-1.9.1 -I/home/wrk
 
 LIBS = "-lpthread -lrt -ldl -lcrypt -lm"
 
-CFLAGS = "-fPIC  -O3 -ggdb -Wextra -Wno-unused-parameter -Wno-parentheses -Wno-long-long -Wno-missing-field-initializers -Werror=pointer-arith -Werror=write-strings  -Werror=implicit-function-declaration  -fPIC -I/usr/share/R/include "
+CFLAGS = "-fPIC  -O3 -ggdb -Wextra -Wno-unused-parameter -Wno-parentheses -Wno-long-long -Wno-missing-field-initializers -Werror=pointer-arith -Werror=write-strings    -fPIC -I/usr/share/R/include "
 
 RUBYARCHDIR = "#{ENV["RUBYARCHDIR"]}"
 LIBRUBYARG_SHARED = "-Wl,-R -Wl,/home/wrk/.rvm/rubies/ruby-1.9.3-p0/lib -L/home/wrk/.rvm/rubies/ruby-1.9.3-p0/lib -lruby"

data/ext/src/biolib_R_map.c

@@ -0,0 +1,37 @@
+
+// #include <stdio.h>
+#include <stdlib.h>
+#include <stdbool.h>
+#include <biolib_error.h>
+#include <biolib_R_map.h>
+
+int R_running = false;
+
+/* 
+ * Initialize the R environment so we can use Rlib.so. 
+ * FIXME: R_HOME is hard coded here.
+ */
+
+void BioLib_R_Init() {
+  char *argv[] = {"BiolibEmbeddedR", "--gui=none", "--silent", "--no-environ" };
+  int argc = sizeof(argv)/sizeof(argv[0]);
+
+  if (!R_running) {
+    biolib_log(LOG_INFO,"Initialize embedded R (library)");
+    setenv("R_HOME","/usr/lib/R",1);
+    Rf_initEmbeddedR(argc, argv);
+    R_running = true;
+  }
+}
+
+/*
+ * Close down R environment
+ */
+
+void BioLib_R_Close() {
+  if (R_running) {
+    Rf_endEmbeddedR(0);
+    R_running = false;
+  }
+}
+

data/ext/src/biolib_R_map.h

@@ -0,0 +1,13 @@
+// Mapping R functions to biolib - used for porting R modules into
+// biolib.
+//
+
+#ifdef BIOLIB
+
+  #include <biolib_error.h>
+
+  // Redefine the R error function
+  #undef error
+  #define error(args...) biolib_fatal(args)
+
+#endif // BIOLIB

data/ext/src/biolib_error.c

@@ -0,0 +1,61 @@
+/* Error and logger functions */
+
+#include <stdio.h>
+#include <stdarg.h>
+#include <biolib_error.h>
+
+static int loglevel = LOG_WARNING;
+static FILE *stdlog = NULL;
+static char *lognames[] = {
+"LOG_EMERG",
+"LOG_ALERT",
+"LOG_CRIT",
+"LOG_ERR", 
+"LOG_WARNING",
+"LOG_NOTICE",
+"LOG_INFO",   
+"LOG_DEBUG" }; 
+
+
+void biolib_fatal(const char *template, ...)
+{
+
+  va_list ap;
+  fprintf (stderr, "BIOLIB FATAL ERROR: ");
+  va_start (ap, template);
+  vfprintf (stderr, template, ap);
+  va_end (ap);
+  fprintf (stderr,"\n");
+
+  exit(4);
+}
+
+/* 
+ * Set the loglevel (defined in biolib_error.h) for the simple logger 
+ */
+
+void biolib_setloglevel(int level)
+{
+  loglevel = level;
+  char buf[256];
+  sprintf(buf,"Setting log level to %d",level);
+  biolib_log(LOG_ALERT,buf);
+}
+
+/*
+ * Simple logger for biolib
+ */
+
+void biolib_log(int level, const char *s)
+{
+  if (level <= loglevel) {
+    if (stdlog==NULL)
+      stdlog = stderr;
+    fprintf(stdlog,"biolib_log (level %d): ",level);
+    fprintf(stdlog,lognames[level]);
+    fprintf(stdlog,": ");
+    fprintf(stdlog,s);
+    fprintf(stdlog,"\n");
+  }
+}
+

data/ext/src/biolib_error.h

@@ -0,0 +1,22 @@
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+#define LOG_EMERG    1
+#define LOG_ALERT    2
+#define LOG_CRIT     3
+#define LOG_ERR      4
+#define LOG_WARNING  5
+#define LOG_NOTICE   6
+#define LOG_INFO     7
+#define LOG_DEBUG    8
+
+void biolib_fatal(const char *e_template, ...);
+void biolib_setloglevel(int level);
+void biolib_log(int level, const char *s);
+
+#ifdef __cplusplus
+}
+#endif
+

data/ext/src/mkrf_conf.rb

@@ -1,6 +1,8 @@
 require 'mkrf'
 Mkrf::Generator.new('libaffyext') do | mkrf |
   mkrf.cflags << `R CMD config --cppflags`.strip
+  # disable these chechs for Ruby 1.9.3
   mkrf.cflags.gsub!(/-Werror=declaration-after-statement/,'')
+  mkrf.cflags.gsub!(/-Werror=implicit-function-declaration/,'')
   mkrf.ldshared << `R CMD config --ldflags`.strip
 end

data/lib/bio/affyext.rb

@@ -3,6 +3,15 @@ module Bio
 
   module Affy
 
+    class CDFProbeSet < FFI::Struct
+      layout :isQC,    :int,
+             :pm_num,  :int,
+             :mm_num,  :int,
+             :pm,      :pointer,
+             :mm,      :pointer,
+             :name,    [:uint8, 64] 
+    end
+
     module Ext
 
       extend FFI::Library
@@ -12,10 +21,14 @@ module Bio
       ffi_convention :stdcall
 
       attach_function :has_affyext, [ :int ], :int
-      # attach_function :open_cdffile, [ :string ], :pointer
-      def open_cdffile s
-      end
-
+      attach_function :BioLib_R_Init, [], :void
+      attach_function :BioLib_R_Close, [], :void
+      attach_function :open_cdffile, [ :string ], :pointer
+      attach_function :open_celfile, [ :string ], :pointer
+      attach_function :cel_intensity, [ :pointer, :int ], :double
+      attach_function :cel_num_intensities, [ :pointer ], :uint64
+      attach_function :cdf_num_probesets, [ :pointer ], :uint64
+      attach_function :cdf_probeset_info, [ :pointer, :int ], :pointer
     end
 
   end

data/spec/bio-affy_spec.rb

@@ -1,22 +1,44 @@
-ROOT = File.dirname(__FILE__)
-$: << File.join([ROOT, "..","lib"])
+ROOT = File.dirname(File.dirname(__FILE__))
+$: << File.join([ROOT, "lib"])
 # ENV['LD_LIBRARY_PATH'] = File.join([ROOT, "..","lib"])
 
 require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
 require 'bio-affy'
 
-DATADIR = ROOT + File.join('test','data','affy')
-CDF = DATADIR+"MG_U74Av2.CDF.gz"
-CEL1 = DATADIR+"GSM103328.CEL.gz"
+DATADIR = File.join([ROOT,'test','data','affy'])
+CDF = File.join(DATADIR,"MG_U74Av2.CDF")
+CDF2 = File.join(DATADIR,"ATH1-121501.CDF")
+CEL1 = File.join(DATADIR,"GSM103328.CEL.gz")
 
 describe "BioAffy" do
   it "should find the shared library" do
     Bio::Affy::Ext.has_affyext(5).should == 60
   end
   it "should open a CDF file" do
-    @cdf = Bio::Affy::Ext.open_cdffile(CDF)
+    Bio::Affy::Ext.BioLib_R_Init()
+    cdf = Bio::Affy::Ext.open_cdffile(CDF)
+    cdf.null?.should == false
+    num_probesets = Bio::Affy::Ext.cdf_num_probesets(cdf)
+    num_probesets.should == 12501
+  end
+  it "should open a CEL file" do
+    cel1 = Bio::Affy::Ext.open_celfile(CEL1)
+    num = Bio::Affy::Ext.cel_num_intensities(cel1)
+    num.should == 409600 
+  end
+  it "should find the probe value for 1511" do
+    cel = Bio::Affy::Ext.open_celfile(CEL1)
+    probe_value = Bio::Affy::Ext.cel_intensity(cel,1510)
+    probe_value.should == 10850.8
+  end
+  it "should name the probes for 1511" do
+    cdf = Bio::Affy::Ext.open_cdffile(CDF)
+    # memptr = MemoryPointer.new :pointer
+    probeset_ptr = Bio::Affy::Ext.cdf_probeset_info(cdf,1510)
+    probeset = Bio::Affy::CDFProbeSet.new(probeset_ptr)
+    probeset[:isQC].should == 0
+    probeset[:pm_num].should == 16
+    probeset[:mm_num].should == 16
+    probeset[:name].to_ptr.read_string.should == "98910_at"
   end
-  it "should open a CEL file"
-  it "should find the probe values"
-  it "should name the probes"
 end

metadata

@@ -1,19 +1,19 @@
 --- !ruby/object:Gem::Specification
 name: bio-affy
 version: !ruby/object:Gem::Version
-  version: 0.1.0.alpha.1
-  prerelease: 6
+  version: 0.5.0
+  prerelease: 
 platform: ruby
 authors:
 - Pjotr Prins
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2011-12-03 00:00:00.000000000 Z
+date: 2011-12-05 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &18461260 !ruby/object:Gem::Requirement
+  requirement: &21542960 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -21,10 +21,10 @@ dependencies:
         version: 2.7.0
   type: :development
   prerelease: false
-  version_requirements: *18461260
+  version_requirements: *21542960
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &18460160 !ruby/object:Gem::Requirement
+  requirement: &21541680 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -32,10 +32,10 @@ dependencies:
         version: 1.0.12
   type: :development
   prerelease: false
-  version_requirements: *18460160
+  version_requirements: *21541680
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &18459540 !ruby/object:Gem::Requirement
+  requirement: &21557520 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -43,10 +43,10 @@ dependencies:
         version: 1.6.4
   type: :development
   prerelease: false
-  version_requirements: *18459540
+  version_requirements: *21557520
 - !ruby/object:Gem::Dependency
   name: rcov
-  requirement: &18458800 !ruby/object:Gem::Requirement
+  requirement: &21557000 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -54,10 +54,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *18458800
+  version_requirements: *21557000
 - !ruby/object:Gem::Dependency
   name: ffi
-  requirement: &18458220 !ruby/object:Gem::Requirement
+  requirement: &21556440 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -65,10 +65,10 @@ dependencies:
         version: 1.0.11
   type: :development
   prerelease: false
-  version_requirements: *18458220
+  version_requirements: *21556440
 - !ruby/object:Gem::Dependency
   name: mkrf
-  requirement: &18457560 !ruby/object:Gem::Requirement
+  requirement: &21555820 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -76,7 +76,7 @@ dependencies:
         version: 0.2.3
   type: :development
   prerelease: false
-  version_requirements: *18457560
+  version_requirements: *21555820
 description: ! "Affymetrix microarray file format parser\n  (CEL/CDF) for Ruby. FFI
   binding to Biolib port of R/Affyio by Benjamin Milo Bolstad"
 email: pjotr.public01@thebird.nl
@@ -102,63 +102,40 @@ files:
 - ext/HISTORY
 - ext/LICENSE
 - ext/NAMESPACE
-- ext/R/check.cdf.type.R
-- ext/R/read.cdffile.list.R
-- ext/R/read.celfile.R
-- ext/R/read.celfile.header.R
-- ext/R/read.probematrices.R
 - ext/README_BIOLIB
 - ext/aclocal.m4
 - ext/configure
 - ext/configure.in
-- ext/man/check.cdf.type.Rd
-- ext/man/read.cdffile.list.Rd
-- ext/man/read.celfile.Rd
-- ext/man/read.celfile.header.Rd
-- ext/man/read.celfile.probeintensity.matrices.Rd
 - ext/src/CMakeLists.txt
 - ext/src/Makevars.in
 - ext/src/Makevars.win
 - ext/src/Rakefile
+- ext/src/biolib_R_map.c
+- ext/src/biolib_R_map.h
 - ext/src/biolib_affyio.c
 - ext/src/biolib_affyio.h
-- ext/src/biolib_affyio.o
+- ext/src/biolib_error.c
+- ext/src/biolib_error.h
 - ext/src/fread_functions.c
 - ext/src/fread_functions.h
-- ext/src/fread_functions.o
-- ext/src/libaffyext.so
-- ext/src/mkrf.log
 - ext/src/mkrf_conf.rb
 - ext/src/read_abatch.c
 - ext/src/read_abatch.h
-- ext/src/read_abatch.o
 - ext/src/read_bpmap.c
-- ext/src/read_bpmap.o
 - ext/src/read_cdf.h
 - ext/src/read_cdf_xda.c
-- ext/src/read_cdf_xda.o
 - ext/src/read_cdffile2.c
-- ext/src/read_cdffile2.o
 - ext/src/read_celfile_generic.c
 - ext/src/read_celfile_generic.h
-- ext/src/read_celfile_generic.o
 - ext/src/read_clf.c
-- ext/src/read_clf.o
 - ext/src/read_generic.c
 - ext/src/read_generic.h
-- ext/src/read_generic.o
 - ext/src/read_pgf.c
-- ext/src/read_pgf.o
 - lib/bio-affy.rb
 - lib/bio/affy.rb
 - lib/bio/affyext.rb
-- lib/bio/libaffyext.so
 - spec/bio-affy_spec.rb
 - spec/spec_helper.rb
-- test/data/affy/GSM103328.CEL.gz
-- test/data/affy/GSM103329.CEL.gz
-- test/data/affy/GSM103330.CEL.gz
-- test/data/affy/MG_U74Av2.CDF.gz
 homepage: http://github.com/pjotrp/bioruby-affy
 licenses:
 - MIT
@@ -174,13 +151,13 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 4468183158933499689
+      hash: -420869817303685437
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements:
-  - - ! '>'
+  - - ! '>='
     - !ruby/object:Gem::Version
-      version: 1.3.1
+      version: '0'
 requirements: []
 rubyforge_project: nowarning
 rubygems_version: 1.8.10

data/ext/R/check.cdf.type.R

@@ -1,18 +0,0 @@
-###
-### File: check.cdf.type.R
-###
-### Aim: return a string giving the file format. Either text, xda or unknown
-###      in the case that file format is not known.
-###
-
-
-check.cdf.type <- function(filename){
-
-  if (.Call("CheckCDFtext",filename,PACKAGE="affyio")){
-    return("text")
-  } else if (.Call("CheckCDFXDA",filename,PACKAGE="affyio")){
-    return("xda")
-  } else {
-    return("unknown")
-  }
-}

data/ext/R/read.cdffile.list.R

@@ -1,23 +0,0 @@
-###
-### File: read.cdffile.list.R
-###
-### Aim: reads full CDF file into R list structure.
-###
-### History
-### Dec 1, 2005 - Initial version
-###
-
-
-read.cdffile.list <- function (filename, cdf.path = getwd()){
-
-  cdf.type <- check.cdf.type(file.path(path.expand(cdf.path),filename))
-  if (cdf.type == "xda"){
-    .Call("ReadCDFFileIntoRList", file.path(path.expand(cdf.path),
-                                            filename), TRUE, PACKAGE = "affyio")
-  } else if (cdf.type =="text"){
-    .Call("ReadtextCDFFileIntoRList", file.path(path.expand(cdf.path),
-                                                filename), TRUE, PACKAGE = "affyio")
-  } else {
-    stop(paste("File format for",filename,"not recognized."))
-  }
-}

data/ext/R/read.celfile.R

@@ -1,11 +0,0 @@
-###
-### File: read.celfile.R
-###
-### Aim: read entire contents of a single given specified CEL file into
-###      an R data structure.
-###
-
-
-read.celfile <- function(filename,intensity.means.only=FALSE){
- return(.Call("R_read_cel_file",filename,intensity.means.only,PACKAGE="affyio"))
-}

data/ext/R/read.celfile.header.R

@@ -1,37 +0,0 @@
-###
-### File: read.celfile.header.R
-###
-### Aim: read header contents of a given specified CEL file into
-###      an R data structure.
-###
-
-
-read.celfile.header <- function(filename,info=c("basic","full"),verbose=FALSE){
-  compress <- FALSE
-
-  info <- match.arg(info)
-
-  if (info == "basic"){
-    if (verbose)
-      cat("Reading", filename, "to get header information.\n")
-    headdetails <- .Call("ReadHeader", filename, PACKAGE="affyio")
-    names(headdetails) <- c("cdfName","CEL dimensions")
-  } else {
-    if (verbose)
-      cat("Reading", filename, "to get full header information.\n")
-    ### full returns greater detailed information from the header. Exact details differ depending on the file format.
-    headdetails <- try(.Call("ReadHeaderDetailed", filename, PACKAGE="affyio"))
-    if (is(headdetails, "try-error"))
-        stop("Failed to get full header information for ", filename)
-    names(headdetails) <- c("cdfName","CEL dimensions","GridCornerUL","GridCornerUR","GridCornerLR","GridCornerLL","DatHeader","Algorithm","AlgorithmParameters","ScanDate")
-
-    if (nchar(headdetails$ScanDate) == 0){
-      # try to extract it from the DatHeader
-      DatHeaderSplit <- strsplit(headdetails$DatHeader," ")
-      Which.Date <- grep("[0-9]*/[0-9]*/[0-9]*",DatHeaderSplit[[1]])
-      Which.Time <-  grep("[0-9]*:[0-9]*:[0-9]*",DatHeaderSplit[[1]])
-      headdetails$ScanDate <- paste(DatHeaderSplit[[1]][Which.Date],DatHeaderSplit[[1]][Which.Time])
-    }
-  }
-  return(headdetails)
-}

data/ext/R/read.probematrices.R

@@ -1,29 +0,0 @@
-###
-### File: read.probematrices.R
-###
-### Aim: read in PM or MM or both probe intensities into a list of
-###       of matrices where the probes for particular probesets are
-###       contiguous in the returned matrix
-###       Each Matrix has probes in rows and arrays in columns
-###
-### Copyright (C) 2005     B. M. Bolstad
-###
-### History
-### Nov 30, 2005 - Initial version
-###
-
-
-read.celfile.probeintensity.matrices <- function(filenames, cdfInfo, rm.mask=FALSE, rm.outliers=FALSE, rm.extra=FALSE, verbose=FALSE, which= c("pm","mm","both")){
-  which <- match.arg(which)
-
-  filenames <- as.character(filenames)
-  if (verbose)
-    cat("Reading", filenames[1], "to get header information.\n")
-  headdetails <- .Call("ReadHeader", filenames[1], PACKAGE="affyio")
-  dim.intensity <- headdetails[[2]]
-  ref.cdfName <- headdetails[[1]]
-  
-  .Call("read_probeintensities", filenames,
-        rm.mask, rm.outliers, rm.extra, ref.cdfName,
-        dim.intensity, verbose, cdfInfo,which, PACKAGE="affyio")
-}

data/ext/man/check.cdf.type.Rd

@@ -1,22 +0,0 @@
-\name{check.cdf.type}
-\alias{check.cdf.type}
-\title{CDF file format function}
-\description{This function returns a text string giving the file format
-  for the supplied filename
-}
-\usage{check.cdf.type(filename)
-}
-\arguments{
-  \item{filename}{fullpath to a cdf file}
-}
-\value{Returns a string which is currently one of:
-
-    \item{text}{the cdf file is of the text format}
-    \item{xda}{the cdf file is of the binary format used in GCOS}
-    \item{unknown}{the parser can not handle this format or does not
-      recognize this file as a CDF file}
-
-  }
-
-\author{B. M. Bolstad <bmb@bmbolstad.com>}
-\keyword{IO}

data/ext/man/read.cdffile.list.Rd

@@ -1,20 +0,0 @@
-\name{read.cdffile.list}
-\alias{read.cdffile.list}
-\title{Read CDF file into an R list}
-\description{This function reads the entire contents of a cdf file into
-  an R list structure
-}
-\usage{read.cdffile.list(filename, cdf.path = getwd())
-}
-\arguments{
-\item{filename}{name of CDF file}
-\item{cdf.path}{path to cdf file}
-}
-\value{returns a \code{list} structure. The exact contents may vary
-depending on the file format of the cdf file (see \code{\link{check.cdf.type}})
-}
-\details{
-Note that this function can be very memory intensive with large CDF files.
-}
-\author{B. M. Bolstad <bmb@bmbolstad.com>}
-\keyword{IO}

data/ext/man/read.celfile.Rd

@@ -1,23 +0,0 @@
-\name{read.celfile}
-\alias{read.celfile}
-\title{Read a CEL file into an R list}
-\description{This function reads the entire contents of a CEL file into
-  an R list structure
-}
-\usage{read.celfile(filename,intensity.means.only=FALSE)
-}
-\arguments{
-\item{filename}{name of CEL file}
-\item{intensity.means.only}{If \code{TRUE} then read on only the MEAN section in INTENSITY}
-}
-\value{returns a \code{list} structure. The exact contents may vary
-depending on the file format of the CEL file
-}
-\details{
-The list has four main items. HEADER, INTENSITY, MASKS, OUTLIERS. Note
-that INTENSITY is a list of three vectors MEAN, STDEV, NPIXELS. HEADER
-is also a list. Both of MASKS and OUTLIERS are matrices.
-
-}
-\author{B. M. Bolstad <bmb@bmbolstad.com>}
-\keyword{IO}

data/ext/man/read.celfile.header.Rd

@@ -1,22 +0,0 @@
-\name{read.celfile.header}
-\alias{read.celfile.header}
-\title{Read header information from cel file}
-\description{
-  This function reads some of the header information (appears before probe
-  intensity data) from the supplied cel file.
-}
-\usage{read.celfile.header(filename,info=c("basic","full"),verbose=FALSE)
-}
-\arguments{
-  \item{filename}{name of CEL file. May be fully pathed}
-  \item{info}{A string. \code{basic} returns the dimensions of the chip
-    and the name of the CDF file used when the CEL file was
-    produced. \code{full} returns more information in greater detail.}
-  \item{verbose}{a \code{\link{logical}}. When true the parsing routine
-    prints more information, typically useful for debugging.}
-}
-\value{
-  A \code{list} data structure.
-}
-\author{B. M. Bolstad <bmb@bmbolstad.com>}
-\keyword{IO}

data/ext/man/read.celfile.probeintensity.matrices.Rd

@@ -1,31 +0,0 @@
-\name{read.celfile.probeintensity.matrices}
-\alias{read.celfile.probeintensity.matrices}
-\title{Read PM or MM from CEL file into matrices}
-\description{This function reads PM, MM or both types of intensities
-  into matrices. These matrices have all the probes for a probeset in
-  adjacent rows
-}
-\usage{read.celfile.probeintensity.matrices(filenames, cdfInfo, rm.mask=FALSE, rm.outliers=FALSE, rm.extra=FALSE, verbose=FALSE, which= c("pm","mm","both"))
-}
-\arguments{
-  \item{filenames}{a character vector of filenames}
-  \item{cdfInfo}{a list with items giving PM and MM locations for
-    desired probesets. In same structure as returned by \code{\link[makecdfenv]{make.cdf.package}}}
-  \item{rm.mask}{a \code{\link{logical}}. Return these probes as NA if
-      there are in the [MASK] section of the CEL file}
-  \item{rm.outliers}{a \code{\link{logical}}. Return these probes as NA if
-      there are in the [OUTLIERS] section of the CEL file}.
-  \item{rm.extra}{a \code{\link{logical}}. Return these probes as NA if
-      there are in the [OUTLIERS] section of the CEL file}.
-  \item{verbose}{a \code{\link{logical}}. When true the parsing routine
-    prints more information, typically useful for debugging.}
-
-  \item{which}{a string specifing which probe type to return}
-  
-}
-\value{returns a \code{\link{list}} of \code{\link{matrix}} items. One
-  matrix contains PM probe intensities, with probes in rows and arrays
-  in columns
-}
-\author{B. M. Bolstad <bmb@bmbolstad.com>}
-\keyword{IO}

data/ext/src/mkrf.log

@@ -1,11 +0,0 @@
-# Logfile created on 2011-12-03 11:33:02 +0100 by logger.rb/31641
-I, [2011-12-03T11:33:02.903130 #3787]  INFO -- : Rakefile written
-I, [2011-12-03T11:34:13.165687 #3885]  INFO -- : Rakefile written
-I, [2011-12-03T11:34:52.961635 #3934]  INFO -- : Rakefile written
-I, [2011-12-03T11:35:50.664883 #3983]  INFO -- : Rakefile written
-I, [2011-12-03T11:36:17.924126 #4032]  INFO -- : Rakefile written
-I, [2011-12-03T11:37:44.903101 #4091]  INFO -- : Rakefile written
-I, [2011-12-03T11:37:56.891896 #4140]  INFO -- : Rakefile written
-I, [2011-12-03T11:42:01.780667 #4246]  INFO -- : Rakefile written
-I, [2011-12-03T11:43:22.916832 #4374]  INFO -- : Rakefile written
-I, [2011-12-03T12:17:14.892390 #24167]  INFO -- : Rakefile written