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| author | Hui Lan <lanhui@zjnu.edu.cn> | 2021-02-19 10:43:24 +0800 |
|---|---|---|
| committer | Hui Lan <lanhui@zjnu.edu.cn> | 2021-02-19 10:43:24 +0800 |
| commit | 2ea63a2ca9778c1154f7d800d3d7a08e78afd8fb (patch) | |
| tree | 5a7039a048e0ec728288f2a986645e636e3fae1f /brain.documentation/QUICKSTART.rst | |
| parent | 20de58ba55ecb36fb8eb1529f263b1ee5c9f2d08 (diff) | |
QUICKSTART.rst: explain option EXISTING_TARGET_TF_PAIRS in parameter_for_net.txt.
Diffstat (limited to 'brain.documentation/QUICKSTART.rst')
| -rw-r--r-- | brain.documentation/QUICKSTART.rst | 3 |
1 files changed, 3 insertions, 0 deletions
diff --git a/brain.documentation/QUICKSTART.rst b/brain.documentation/QUICKSTART.rst index 3ead79c..ada02d8 100644 --- a/brain.documentation/QUICKSTART.rst +++ b/brain.documentation/QUICKSTART.rst @@ -802,6 +802,7 @@ Once any of the following files is modified, update the network using the follow %%INPUT_MATRIX=../Data/history/bind/INPUT_binding.txt
%%BINDING_INFO=../Data/parameter/parameter_for_buildCmatrix.txt
%%EXPRESSION_INFO=../Data/parameter/parameter_for_buildRmatrix.txt
+ %%EXISTING_TARGET_TF_PAIRS=../Data/information/target_tf_agris.txt ../Data/information/target_tf.txt.20170629_143000
%%MAX_NUM_TARGETS=200
%%OVERFLOW_TARGETS_PERCENTAGE=0.25
%%HIGH_PRIORITY_GENE=AT3G26744 AT2G43790 AT3G18550
@@ -814,6 +815,8 @@ Once any of the following files is modified, update the network using the follow - MAX_NUM_TARGETS and OVERFLOW_TARGETS_PERCENTAGE are used in make_target_tf.py.
+ - EXISTING_TARGET_TF_PAIRS -- specify files including tf-target pairs from other sources (if any). Sources are separated by a space. The user could create such files to include tf-target interaction hypotheses that need to be further investigated by brain using RNA-Seq data.
+
- HOLDON -- if YES, updates in this file won't take effect. See update_network.py for detail.
- EXPRESSION_MATRIX_DESCRIPTION -- if this parameter is specified, then the last field (tissue or method) of edges created by create_edges0.py will be this description (e.g., drought).
|