[Genabel-commits] r1158 - in pkg/OmicABEL: . doc
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Mar 19 16:42:12 CET 2013
Author: dfabregat
Date: 2013-03-19 16:42:11 +0100 (Tue, 19 Mar 2013)
New Revision: 1158
Added:
pkg/OmicABEL/doc/HOWTO
Removed:
pkg/OmicABEL/doc/HowTo
Modified:
pkg/OmicABEL/DISCLAIMER.Linux
pkg/OmicABEL/README
pkg/OmicABEL/doc/INSTALL
Log:
HowTo renamed to HOWTO
Fixed some details in the documentation
Modified: pkg/OmicABEL/DISCLAIMER.Linux
===================================================================
--- pkg/OmicABEL/DISCLAIMER.Linux 2013-03-18 10:08:45 UTC (rev 1157)
+++ pkg/OmicABEL/DISCLAIMER.Linux 2013-03-19 15:42:11 UTC (rev 1158)
@@ -1,6 +1,7 @@
-The Linux precompiled binary for CLAK-GWAS provided in this package
-includes libraries distributed under their respective licenses.
-This is the case for the Intel (R) Math Kernel Library (MKL).
-Under the terms of the Intel MKL License we redistribute
-computational portions of Intel MKL with our software to
+The CLAK-GWAS precompiled binary (for Linux) provided in this package
+includes libraries distributed under their respective licenses.
+This is the case for the Intel (R) Math Kernel Library (MKL).
+Under the terms of the Intel MKL License, we redistribute
+computational portions of Intel MKL with our software to
improve the user experience.
+
Modified: pkg/OmicABEL/README
===================================================================
--- pkg/OmicABEL/README 2013-03-18 10:08:45 UTC (rev 1157)
+++ pkg/OmicABEL/README 2013-03-19 15:42:11 UTC (rev 1158)
@@ -13,14 +13,16 @@
1. INSTALLATION
----------------
-Please see the doc/INSTALL file (only necessary if you didn't download a
-precompiled version).
+Please see the doc/INSTALL file.
+Note that if you downloaded one of the binary versions, no
+installation is needed.
+
2. USING CLAK-GWAS
-------------------
-Please see the doc/HowTo file.
+Please see the doc/HOWTO file.
3. KNOWN ISSUES
@@ -32,15 +34,15 @@
( fabregat [at] aices [dot] rwth-aachen [dot] de ); we will attend
your request as soon as possible.
-3.2 Currently, we only support input data in DenABEL (filevector) data format
- and double precision datatype. We are working on the support for
- more datatypes.
+3.2 Currently, the input data must consist of double precision entries,
+ organized according to the DatABEL (filevector) data format.
+ We are working on the support for more datatypes.
4. CONTACT
-----------
-For any question, request, suggestion, or comment, please free to contact us:
+For any question, request, suggestion, or comment, please contact us:
Diego Fabregat Traver, fabregat [at] aices [dot] rwth-aachen [dot] de
Paolo Bientinesi, pauldj [at] aices [dot] rwth-aachen [dot] de
Added: pkg/OmicABEL/doc/HOWTO
===================================================================
--- pkg/OmicABEL/doc/HOWTO (rev 0)
+++ pkg/OmicABEL/doc/HOWTO 2013-03-19 15:42:11 UTC (rev 1158)
@@ -0,0 +1,86 @@
+1. Who is Whom
+---------------
+
+In the directory bin/, you 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, as input CLAK-GWAS only accepts data files in the DatABEL
+(filevector) format. Examples of how to transform your data into
+filevector are given in the tutorial available at
+
+http://www.genabel.org/packages/OmicABEL
+
+If you need help, please contact us, or use the GenABEL project forum
+
+http://forum.genabel.org
+
+
+3. Running GWAS analyses
+-------------------------
+
+The tutorial available at
+
+http://www.genabel.org/packages/OmicABEL
+
+also provides a basic example on the use of OmicABEL to run GWAS analyses.
+Here we detail the options of CLAK-GWAS. The complete list of options is
+available through the command
+
+
+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 <arguments> [options]
+
+Following arguments are mandatory:
+
+ -cov <path> base path to the file containing the covariates
+ -phi <path> base path to the file containing the relationship matrix
+ -snp <path> base path to the file containing the SNPs
+ -pheno <path> base path to the file containing the phenotypes
+ -out <path> base path to the file where the output will be stored
+
+Following options might be given:
+
+ -var [chol | eigen] Default is chol.
+ -nths <num> Default is 1 thread.
+ -thres <num> 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 specify 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 specify the output file(s)
+
+* "-nths" allows the user to specify how many cores to use.
+
+* "-thres" is used to specify the acceptable proportion of missing values.
+ It must be an integer value between 1 and 100.
+ (the missing values are imputed by means, therefore our suggestion
+ is to keep this threshold at 95 at minimum).
+
+
+For a detailed description of "reshuffle", please refer to doc/README-reshuffle
Deleted: pkg/OmicABEL/doc/HowTo
===================================================================
--- pkg/OmicABEL/doc/HowTo 2013-03-18 10:08:45 UTC (rev 1157)
+++ pkg/OmicABEL/doc/HowTo 2013-03-19 15:42:11 UTC (rev 1158)
@@ -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 doc/README-reshuffle
Modified: pkg/OmicABEL/doc/INSTALL
===================================================================
--- pkg/OmicABEL/doc/INSTALL 2013-03-18 10:08:45 UTC (rev 1157)
+++ pkg/OmicABEL/doc/INSTALL 2013-03-19 15:42:11 UTC (rev 1158)
@@ -1,29 +1,30 @@
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:
+ Our software requires the BLAS and LAPACK. If they are not available
+ in your system, you can freely download them, for example, from:
* BLAS: http://xianyi.github.com/OpenBLAS/
* LAPACK: http://netlib.org/lapack/#_software
-
+
Their installation is typically rather straightforward.
+ Please, keep in mind that it is important to install an optimized
+ version of BLAS, be it OpenBLAS or a different one.
+
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.
+ The file make.inc sets a number of environment variables necessary
+ for the compilation. The directory inc/ contains several versions of
+ make.inc, customized for different combinations of architectures,
+ compilers, and libraries. Choose the most suitable one for you, 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.
+ 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.
More information about the Genabel-commits
mailing list