Name: Predict-TF-Preference
Owner: Duke Center for Genomic and Computational Biology
Description: R scripts to predict preferences between two TFs using data from predict-tf-binding
Created: 2016-09-01 15:57:20.0
Updated: 2016-11-04 04:32:04.0
Pushed: 2017-03-06 16:42:11.0
Homepage: null
Size: 9615
Language: R
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R scripts to predict preferences between two TFs using data from predict-tf-binding
This script is designed to extract binding probabilities out of BED files generated by Predict-TF-Binding.
./predict-tf-preference.R tf1 tf2 tf1.bed tf2.bed prefs.bed
Where:
tf1
is the name of the first transcription factor (e.g. E2f1)tf2
is the name of the second transcription factor (e.g. E2f4)tf1.bed
is a bed file containing prediction scores for the first TFtf2.bed
is a bed file containing prediction scores for the second TFprefs.bed
is the name of the output file you'd like to write.This script is designed to remove preference scores favoring a TF where the binding prediction was below a NegCtrl threshold
./filter-preference-threshold.py --spaces tf1.bed tf2.bed prefs.bed tf1_threshold tf2_threshold
Where:
tf1.bed
is a bed file containing prediction scores for the first TFtf2.bed
is a bed file containing prediction scores for the second TFtf1_threshold
is the NegCtrl threshold value (float) for tf1tf2_threshold
is the NegCtrl threshold value (float) for tf2prefs.bed
is the preferences generated by predict-tf-preference.R