diff --git a/.github/workflows/python-publish.yml b/.github/workflows/python-publish.yml index ec70354..c1000d2 100644 --- a/.github/workflows/python-publish.yml +++ b/.github/workflows/python-publish.yml @@ -18,7 +18,7 @@ permissions: jobs: deploy: - runs-on: ubuntu-latest + runs-on: self-hosted steps: - uses: actions/checkout@v3 diff --git a/README.md b/README.md index 3e595c1..c795c7a 100644 --- a/README.md +++ b/README.md @@ -34,7 +34,7 @@ The patients id or samples ids must be the same in the "expression_data" and "m In the condition column of the meta DataFrame, the control samples should be encoded as 0 and case samples as 1. -GRN network should be provided a prior, You can either use an experimental validated GRN or learn it from control samples, we recommend using software like [arboreto](https://github.com/aertslab/arboreto), since you can use its output directly to DysRegNet. +The gene regulatory network should be provided by the user. You can either use an experimental validated GRN or learn it from control samples. We recommend using software like [arboreto](https://github.com/aertslab/arboreto) since you can use its output directly to DysRegNet. @@ -53,9 +53,9 @@ Additionally, you can provide the following parameters: - ConCov: List of continuous covariates. They should match the name of their columns in the meta Dataframe. -- zscoring: Boolean, default: True. zscoring of expression data (if needed). +- zscoring: Boolean, default: False. zscoring of expression data (if needed). -- bonferroni_alpha:P-value threshold for multiple testing correction +- bonferroni_alpha: P-value threshold for multiple testing correction - normaltest: Boolean. If True, Run a normality test for residuals "scipy.stats.normaltest". If residuals are not normal, the edge will not be considered in the analysis. @@ -63,13 +63,13 @@ Additionally, you can provide the following parameters: - R2_threshold: R-squared (R2) threshold from 0 to 1 (optional). If the fit is weaker, the edge will not be considered in the analysis. -- direction_condition: Boolean. If True: only include dysregulation that are relevant for the interactions (down regulation of an activation or up regulation of a supressions). Please check the paper for more details. +- direction_condition: Boolean. If True: only include dysregulation that are relevant for the interactions (down-regulation of an activation or up-regulation of a supressions). Please check the paper for more details. ## Get Started -Please note, that the functions are annotated with dockstrings for more details. +Please note that the functions are annotated with dockstrings for more details. Import the package and pandas: @@ -127,11 +127,11 @@ The expected run time for the installation and running the demo dataset on a "no ## The output -The package output a DataFrame that represents patient-specific dysregulated edges. The columns represent edges and the rows patient ids. +The package outputs a data frame that represents patient-specific dysregulated edges. The columns represent edges, and the rows are patient IDs. In the result table, a value of 0 means that the edge is not significantly dysregulated (different from control samples). Otherwise, the z-score is reported, with a positive in case of activation and a negative sign in case of repression (different than the sign of the residual). -The method "get_results_binary()", outputs binarized dysregulations instead of z-scores. +The method "get_results_binary()" outputs binarized dysregulations instead of z-scores. ## Example diff --git a/setup.py b/setup.py index 227998b..5dd849f 100644 --- a/setup.py +++ b/setup.py @@ -11,7 +11,7 @@ setup(name='dysregnet', - version='0.0.4', + version='0.0.5', description='DysRegNet', long_description=README, long_description_content_type="text/markdown", @@ -24,6 +24,8 @@ "Programming Language :: Python :: 3.7", "Programming Language :: Python :: 3.8", "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", "License :: OSI Approved :: GNU General Public License v3 (GPLv3)", "Topic :: Scientific/Engineering :: Bio-Informatics", ], diff --git a/src/dysregnet/functions.py b/src/dysregnet/functions.py index 22d8a49..29b5543 100644 --- a/src/dysregnet/functions.py +++ b/src/dysregnet/functions.py @@ -105,7 +105,7 @@ def dyregnet_model(data): # condition of direction cond = True - direction = np.sign(results.params[1]) + direction = np.sign(results.params.iloc[1]) # two sided p_value as default