Updated documentation

pgxcentre · Feb 10, 2017 · 9960fe1 · 9960fe1
2 parents 7b218aa + 8038bdc
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diff --git a/README.mkd b/README.mkd
@@ -132,7 +132,7 @@ usage: genipe-launcher [-h] [-v] [--debug] [--thread THREAD] --bfile PREFIX
                        [--report-background BACKGROUND]
 
 Execute the genome-wide imputation pipeline. This script is part of the
-'genipe' package, version 1.3.1.
+'genipe' package, version 1.3.2.
 
 optional arguments:
   -h, --help            show this help message and exit
@@ -277,7 +277,7 @@ usage: imputed-stats [-h] [-v] {cox,linear,logistic,mixedlm,skat} ...
 
 Performs statistical analysis on imputed data (either SKAT analysis, or
 linear, logistic or survival regression). This script is part of the 'genipe'
-package, version 1.3.1.
+package, version 1.3.2.
 
 optional arguments:
   -h, --help            show this help message and exit

diff --git a/docs/index.rst b/docs/index.rst
@@ -69,7 +69,7 @@ Usage
                           [--report-background BACKGROUND]
 
    Execute the genome-wide imputation pipeline. This script is part of the
-   'genipe' package, version 1.3.1.
+   'genipe' package, version 1.3.2.
 
    optional arguments:
      -h, --help            show this help message and exit

diff --git a/docs/installation.rst b/docs/installation.rst
@@ -29,6 +29,11 @@ management):
 * ``pyfaidx`` version 0.3.7 or latest
 * ``drmaa`` version 0.7.6 or latest
 
+.. note::
+
+   Note that ``statsmodels`` (specifically MixedLM analysis) version 0.6
+   **is not compatible** with ``numpy`` version 1.12 and latest.
+
 .. note::
 
    Only Python version 3.4 and higher are supported.

diff --git a/docs/tutorials/tutorial_SKAT.rst b/docs/tutorials/tutorial_SKAT.rst
@@ -334,7 +334,7 @@ the console:
                              {continuous,discrete} [--skat-o] --pheno-name NAME
 
    Uses the SKAT R package to analyze user defined gene sets. This script is part
-   of the 'genipe' package, version 1.3.1.
+   of the 'genipe' package, version 1.3.2.
 
    optional arguments:
      -h, --help            show this help message and exit

diff --git a/docs/tutorials/tutorial_cox.rst b/docs/tutorials/tutorial_cox.rst
@@ -222,7 +222,7 @@ in the console:
                             NAME
 
    Performs a survival regression on imputed data using Cox's proportional hazard
-   model. This script is part of the 'genipe' package, version 1.3.1.
+   model. This script is part of the 'genipe' package, version 1.3.2.
 
    optional arguments:
      -h, --help            show this help message and exit

diff --git a/docs/tutorials/tutorial_extract.rst b/docs/tutorials/tutorial_extract.rst
@@ -237,7 +237,7 @@ analysis in the console:
                             [--rate FLOAT] [--info FLOAT]
 
    Extract imputed markers located in a specific genomic region. This script is
-   part of the 'genipe' package, version 1.3.1.
+   part of the 'genipe' package, version 1.3.2.
 
    optional arguments:
      -h, --help            show this help message and exit

diff --git a/docs/tutorials/tutorial_linear.rst b/docs/tutorials/tutorial_linear.rst
@@ -235,7 +235,7 @@ analysis in the console:
                                --pheno-name NAME
 
    Performs a linear regression (ordinary least squares) on imputed data. This
-   script is part of the 'genipe' package, version 1.3.1.
+   script is part of the 'genipe' package, version 1.3.2.
 
    optional arguments:
      -h, --help            show this help message and exit

diff --git a/docs/tutorials/tutorial_logistic.rst b/docs/tutorials/tutorial_logistic.rst
@@ -224,7 +224,7 @@ regression analysis in the console:
                                  --pheno-name NAME
 
    Performs a logistic regression on imputed data using a GLM with a binomial
-   distribution. This script is part of the 'genipe' package, version 1.3.1.
+   distribution. This script is part of the 'genipe' package, version 1.3.2.
 
    optional arguments:
      -h, --help            show this help message and exit

diff --git a/docs/tutorials/tutorial_mixedlm.rst b/docs/tutorials/tutorial_mixedlm.rst
@@ -266,7 +266,7 @@ effects analysis in the console:
    Performs a linear mixed effects regression on imputed data using a random
    intercept for each group. A p-value approximation is performed so that
    computation time is acceptable for imputed data. This script is part of the
-   'genipe' package, version 1.3.1.
+   'genipe' package, version 1.3.2.
 
    optional arguments:
      -h, --help            show this help message and exit