Name: pathmark-scripts
Owner: UCSC Cancer Research
Description: null
Created: 2012-10-05 20:01:50.0
Updated: 2015-02-19 22:13:03.0
Pushed: 2015-02-19 22:13:02.0
Size: 24517
Language: JavaScript
GitHub Committers
| User | Most Recent Commit | # Commits |
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Other Committers
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2.0
Sam Ng and Joshua M. Stuart
xyPATHMARK.py [options] data_matrix phenotype_matrix pathway_file
_matrix - sample by feature data file
otype_matrix - phenotype by sample dichotomy file
way_file - PARADIGM pathway interactions file
ootstrap_size - number of bootstrap sample to be generated for robustness estimation
ull_size - number of null samples to be generated for significance estimation
ull_permute - permutation method for null model
ignature_method - differential method for computing signatures
ilter_parameters - filter threshold coefficients
iffusion_time - heat diffusion time for signature scores across the network
apply hub filter that includes hubs with high representation of its children
andom_seed - fix random seed
lePlot.py [options] output_directory input_matrix [input_matrix ...]
ut_directory - path to directory to output plots
t_matrix - sample by feature data matrix for plots, rings created from inner to outer
ample_file - one column file of samples to plot
eature_file - one column file of features to plot
rder_parameters - feature:file[,file ...] hierarchical sort on feature and data files
enter_file - two column file of feature scores for center circle colors
olor_map - color parameters file
ile_extension - output file extension (default: png)
output feature names for each plot
Feature requests, comments and requests for clarification should all be sent to the author at sng@soe.ucsc.edu. I will try to respond quickly to all requests, so feel free to email me!