[Genabel-commits] r1156 - in pkg/OmicABEL: . doc
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun Mar 17 17:13:05 CET 2013
Author: dfabregat
Date: 2013-03-17 17:13:04 +0100 (Sun, 17 Mar 2013)
New Revision: 1156
Added:
pkg/OmicABEL/doc/HowTo
pkg/OmicABEL/doc/INSTALL
pkg/OmicABEL/doc/README-reshuffle
Removed:
pkg/OmicABEL/HowTo
pkg/OmicABEL/INSTALL
Modified:
pkg/OmicABEL/Makefile
pkg/OmicABEL/README
Log:
Fixing the structure and completing the "make bindist" option.
The Makefile needs to be improved. Will do later on.
Deleted: pkg/OmicABEL/HowTo
===================================================================
--- pkg/OmicABEL/HowTo 2013-03-17 15:56:41 UTC (rev 1155)
+++ pkg/OmicABEL/HowTo 2013-03-17 16:13:04 UTC (rev 1156)
@@ -1,79 +0,0 @@
-1. Who is Who
---------------
-
-In the bin/ directory you can find the following executables:
-
-* CLAK-GWAS: the program to run GWAS analyses (through CLAK-Chol or CLAK-Eig)
-* reshuffle: the program to extract the output of CLAK-GWAS into text format
-
-The output produced by CLAK-GWAS is kept in a compact binary format
-for performance reasons. The user can then use "reshuffle" to
-extract the desired information. Since the output may be very large,
-reshuffle allows the selection of specific ranges of SNPs and traits.
-
-
-2. Preparing your data
------------------------
-
-Currently, CLAK-GWAS only accepts as input data files in DenABEL
-(filevector) format.
-In the tutorial available in the project's webpage:
-
-http://www.genabel.org/packages/OmicABEL
-
-you can find an example of how to transform your data into filevector.
-If you need help, don't hesitate contacting us or ask for help at the
-GenABEL project forum
-
-http://forum.genabel.org
-
-
-3. Running GWAS analyses
--------------------------
-
-The example in the tutorial also provides a basic example on using OmicABEL
-to run your GWAS analyses. Here we detail the options of CLAK-GWAS.
-The complete list of options for CLAK-GWAS is avaliable through the command
-
-./CLAK-GWAS -h
-
-Usage: CLAK-GWAS [options]
-
-Following options may be given:
-
- -var [chol | eigen] Default is chol.
- -cov base path to covariates file
- -phi base path to kinship matrix file
- -snp base path to SNPs file
- -pheno base path to phenotypes file
- -out base path to output file
- -nths # Default is 1 thread.
- -thres # Default is 95%.
- -h Show this help and exit
-
-* The option "-var" selects the algorithm to use:
- "chol" forces CLAK-GWAS to use the CLAK-Chol algorithm (recommended for
- single-phenotype GWAS).
- "eigen" forces CLAK-GWAS to use the CLAK-Eig algorithms (recommended for
- multiple-phenotype GWAS).
-
-* "-cov", "-phi", "-snp", "-pheno" are used to indicate the input files
- for the analysis. If the covariates are stored in the pair of
- file "covs.fvd" and "covs.fvi", the option -cov
- is used as: "-cov covs". Same for the other three options.
-
-* "-out" is used to indicate the output file(s)
-
-* "-nths" allows the user to indicate how many cores to use.
-
-* "-thres" is the acceptable proportion of missing values
- (these are imputed by means, therefore our suggestion
- is to keep this threshold at 95 at minimum).
-
-
-Options without a default value (-cov, -phi, -snp, -pheno, -out)
-are mandatory.
-
-
-For a detail description of the options for "reshuffle", please
-see src/reshuffle/README.txt
Deleted: pkg/OmicABEL/INSTALL
===================================================================
--- pkg/OmicABEL/INSTALL 2013-03-17 15:56:41 UTC (rev 1155)
+++ pkg/OmicABEL/INSTALL 2013-03-17 16:13:04 UTC (rev 1156)
@@ -1,29 +0,0 @@
-1. Pre-requisites
-------------------
-
- Our software requires the availability of the BLAS and LAPACK
- libraries. If you do not have them installed in your system,
- you can freely downloaded them from:
-
- * BLAS: http://xianyi.github.com/OpenBLAS/
- * LAPACK: http://netlib.org/lapack/#_software
-
- Their installation is typically rather straightforward.
-
-
-2. Compiling
--------------
-
- The file make.inc sets a number of environment variables
- necessary for the compilation. We provide a number of examples
- of this file in the inc/ directory, for different combinations
- of architectures, compilers, and libraries. You can choose the
- most suitable and overwrite the file make.inc with it.
- For instance, if you chose to install the BLAS and LAPACK libraries
- linked above in a linux machine, select the file "make.inc.gnu-goto".
- You will need to set the paths to the aforementioned libraries
- in your system.
-
- Once the make.inc file is ready, you can compile the code.
- Simply type "make" and it will create the binaries "CLAK-GWAS"
- and "reshuffle" in the bin/ directory.
Modified: pkg/OmicABEL/Makefile
===================================================================
--- pkg/OmicABEL/Makefile 2013-03-17 15:56:41 UTC (rev 1155)
+++ pkg/OmicABEL/Makefile 2013-03-17 16:13:04 UTC (rev 1156)
@@ -31,13 +31,18 @@
cd $(RESH_SRCDIR)
$(CXX) $^ -o $@
+# Dirty, improve
+platform=Linux
+bindistDir=OmicABEL-$(platform)-bin
bindist: ./bin/ $(CLAKGWAS) $(RESHUFFLE)
- mkdir OmicABEL-bin
- mkdir OmicABEL-bin/bin/
- cp -a $(CLAKGWAS) $(RESHUFFLE) OmicABEL-bin/bin/
- cp -a COPYING LICENSE OmicABEL-bin
- tar -czvf OmicABEL-bin.tgz OmicABEL-bin
- rm -rf OmicABEL-bin/
+ mkdir $(bindistDir)
+ mkdir $(bindistDir)/bin/
+ mkdir $(bindistDir)/doc/
+ cp -a $(CLAKGWAS) $(RESHUFFLE) $(bindistDir)/bin/
+ cp -a COPYING LICENSE README DISCLAIMER.$(platform) $(bindistDir)
+ cp -a doc/README-reshuffle doc/INSTALL doc/HowTo $(bindistDir)/doc
+ tar -czvf $(bindistDir).tgz $(bindistDir)
+ rm -rf $(bindistDir)
clean:
$(RM) $(OBJS)
Modified: pkg/OmicABEL/README
===================================================================
--- pkg/OmicABEL/README 2013-03-17 15:56:41 UTC (rev 1155)
+++ pkg/OmicABEL/README 2013-03-17 16:13:04 UTC (rev 1156)
@@ -13,14 +13,14 @@
1. INSTALLATION
----------------
-Please see the INSTALL file (only necessary if you didn't download a
+Please see the doc/INSTALL file (only necessary if you didn't download a
precompiled version).
2. USING CLAK-GWAS
-------------------
-Please see the HowTo file.
+Please see the doc/HowTo file.
3. KNOWN ISSUES
Added: pkg/OmicABEL/doc/HowTo
===================================================================
--- pkg/OmicABEL/doc/HowTo (rev 0)
+++ pkg/OmicABEL/doc/HowTo 2013-03-17 16:13:04 UTC (rev 1156)
@@ -0,0 +1,79 @@
+1. Who is Who
+--------------
+
+In the bin/ directory you can find the following executables:
+
+* CLAK-GWAS: the program to run GWAS analyses (through CLAK-Chol or CLAK-Eig)
+* reshuffle: the program to extract the output of CLAK-GWAS into text format
+
+The output produced by CLAK-GWAS is kept in a compact binary format
+for performance reasons. The user can then use "reshuffle" to
+extract the desired information. Since the output may be very large,
+reshuffle allows the selection of specific ranges of SNPs and traits.
+
+
+2. Preparing your data
+-----------------------
+
+Currently, CLAK-GWAS only accepts as input data files in DenABEL
+(filevector) format.
+In the tutorial available in the project's webpage:
+
+http://www.genabel.org/packages/OmicABEL
+
+you can find an example of how to transform your data into filevector.
+If you need help, don't hesitate contacting us or ask for help at the
+GenABEL project forum
+
+http://forum.genabel.org
+
+
+3. Running GWAS analyses
+-------------------------
+
+The example in the tutorial also provides a basic example on using OmicABEL
+to run your GWAS analyses. Here we detail the options of CLAK-GWAS.
+The complete list of options for CLAK-GWAS is avaliable through the command
+
+./CLAK-GWAS -h
+
+Usage: CLAK-GWAS [options]
+
+Following options may be given:
+
+ -var [chol | eigen] Default is chol.
+ -cov base path to covariates file
+ -phi base path to kinship matrix file
+ -snp base path to SNPs file
+ -pheno base path to phenotypes file
+ -out base path to output file
+ -nths # Default is 1 thread.
+ -thres # Default is 95%.
+ -h Show this help and exit
+
+* The option "-var" selects the algorithm to use:
+ "chol" forces CLAK-GWAS to use the CLAK-Chol algorithm (recommended for
+ single-phenotype GWAS).
+ "eigen" forces CLAK-GWAS to use the CLAK-Eig algorithms (recommended for
+ multiple-phenotype GWAS).
+
+* "-cov", "-phi", "-snp", "-pheno" are used to indicate the input files
+ for the analysis. If the covariates are stored in the pair of
+ file "covs.fvd" and "covs.fvi", the option -cov
+ is used as: "-cov covs". Same for the other three options.
+
+* "-out" is used to indicate the output file(s)
+
+* "-nths" allows the user to indicate how many cores to use.
+
+* "-thres" is the acceptable proportion of missing values
+ (these are imputed by means, therefore our suggestion
+ is to keep this threshold at 95 at minimum).
+
+
+Options without a default value (-cov, -phi, -snp, -pheno, -out)
+are mandatory.
+
+
+For a detail description of the options for "reshuffle", please
+see doc/README-reshuffle
Added: pkg/OmicABEL/doc/INSTALL
===================================================================
--- pkg/OmicABEL/doc/INSTALL (rev 0)
+++ pkg/OmicABEL/doc/INSTALL 2013-03-17 16:13:04 UTC (rev 1156)
@@ -0,0 +1,29 @@
+1. Pre-requisites
+------------------
+
+ Our software requires the availability of the BLAS and LAPACK
+ libraries. If you do not have them installed in your system,
+ you can freely downloaded them from:
+
+ * BLAS: http://xianyi.github.com/OpenBLAS/
+ * LAPACK: http://netlib.org/lapack/#_software
+
+ Their installation is typically rather straightforward.
+
+
+2. Compiling
+-------------
+
+ The file make.inc sets a number of environment variables
+ necessary for the compilation. We provide a number of examples
+ of this file in the inc/ directory, for different combinations
+ of architectures, compilers, and libraries. You can choose the
+ most suitable and overwrite the file make.inc with it.
+ For instance, if you chose to install the BLAS and LAPACK libraries
+ linked above in a linux machine, select the file "make.inc.gnu-goto".
+ You will need to set the paths to the aforementioned libraries
+ in your system.
+
+ Once the make.inc file is ready, you can compile the code.
+ Simply type "make" and it will create the binaries "CLAK-GWAS"
+ and "reshuffle" in the bin/ directory.
Added: pkg/OmicABEL/doc/README-reshuffle
===================================================================
--- pkg/OmicABEL/doc/README-reshuffle (rev 0)
+++ pkg/OmicABEL/doc/README-reshuffle 2013-03-17 16:13:04 UTC (rev 1156)
@@ -0,0 +1,79 @@
+Reshuffle ver 0.000
+
+Parameters:
+
+For the first it should be file name without iout and out extensions:
+ (--B_eigen_1000)
+ if your files are B_eigen.iout and B_eigen.out
+
+Data dimensions
+ (--datadims) Gives back t, m, p
+output: "datadims.txt"
+
+SNP names
+ default: (--snpnames) : all
+ by index (--snpnames=27) : name of snp#27
+ by index range, combination (--snpnames=27,2-12,4-20) : name of snp #2-20,27
+output: "snpnames.txt"
+
+Trait names
+ default (--traitnames): all
+ by index (--traitnames=27) : name of trait #27
+ by index range, combination (--traitnames=27,2-12,15)
+output: "traitnames.txt"
+
+Heritabilities, sigma, res_sigma, estimates
+ Default: (--heritabilities) : all traits
+ Reange,indexes (--heritabilities=1-10,4,5-12) : for traits #1-12
+ trait's names (--heritabilities=hgta,hdla) : for traits hgta,hdla
+ regexp in trait's names (--heritabilities=regexp=t) : for traits, in the start of which is "t" : tga,tca (in data_4test)
+ all combinations (--heritabilities=1-10,4,5-12,hgta,lipid_tca,regexp=lipid_)
+output: "estimates.txt"
+Results - association
+ by SNP
+ Dafault (--snp) : for all snp for all traits
+ indexes, ranges (--snp=12,100-1000,500-10000,22000) : for all traits
+ names (--snp=rs3121561,rs6687776) : for snps rs3121561,rs6687776
+ names+around (--snp=rs3121561,rs6687776,before=10,after=15)
+ for (-10,9,...,-1,rs3121561,1,2,...,15,16) + (-10,9,...,-1,rs6687776,1,2,...,15,16)
+ indexes+names+focus (--snp=1-20,50,rs3121561,rs6687776,before=10,after=15)
+ for snps : #1-20,50 + (-10,9,...,-1,rs324001,1,2,...,15,16) + (-10,9,...,-1,rs123123,1,2,...,15,16)
+ NB!: focus only for snp's names, not for indexes
+ output: "data.txt"
+ by trait
+ Dafault (--trait) : for all snp for all traits
+ indexes,range (--trait=1-10,12) : for snp #12 for all traits
+ by names (--traits=tca,hdla) : for traits tca,hdla
+ regexp in trait's names (traits=regexp=lipids_) : for all traits, which name in the beginig has "lipids_"
+ all combinations
+ output: "data.txt"
+ Chi2 more than some threshold
+ (--chi=20) for snps,which chi>20 for all traits
+ output: "chi_data.txt"
+ All combinations of traits,snps, Chi2
+ (--traits=1-2--snps=1-1000--chi=15) for traits #1-2 for snps#1-1000, which chi>15
+ output: "chi_data.txt"
+
+Just write data with chi
+ (--chi) : write data(with chi column) for all snps for all traits
+ all combinations are supported
+ output: "chi_data.txt"
+Dataslim
+ Creating a sub-matrix by Chi2>X (--chi=X--dataslim)
+ output: "slim_data.txt"
+
+Test
+ (--test) run all tests
+ output: test.txt
+
+Info
+ (--info) write some information about programm's run
+
+Examples:
+Reshuffle.exe B_1112_NA_clear_RNA_nocovar --traitnames=1-4,1--snpnames=1-10,20-30,46--traits=1--snps=1-100
+
+outputs from B_1112_NA_clear_RNA_nocovar.iout and B_1112_NA_clear_RNA_nocovar.out:
+
+ traitnames.txt : with trait's names hgta,tga,tca,ldla
+ snpnames.txt Names of snps #1-10,20-30,46
+ trait_hgta.txt : result of association for trait "hgta" for snps #1-100
\ No newline at end of file
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