From 2ea63a2ca9778c1154f7d800d3d7a08e78afd8fb Mon Sep 17 00:00:00 2001 From: Hui Lan Date: Fri, 19 Feb 2021 10:43:24 +0800 Subject: QUICKSTART.rst: explain option EXISTING_TARGET_TF_PAIRS in parameter_for_net.txt. --- brain.documentation/QUICKSTART.rst | 3 +++ 1 file changed, 3 insertions(+) (limited to 'brain.documentation') 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). -- cgit v1.2.1