NAME

       ChromImpute - Large-scale systematic epigenome imputation

SYNOPSIS

       java -Xmx[GB]g -jar /usr/share/java/chromimpute.jar [options]

DESCRIPTION

       ChromImpute  is  software for large-scale systematic epigenome imputation.  ChromImpute takes an existing
       compendium of epigenomic data and uses it to predict  signal  tracks  for  mark-sample  combinations  not
       experimentally mapped or to generate a potentially more robust version of data sets that have been mapped
       experimentally. ChromImpute bases its predictions on features from signal tracks of other marks that have
       been  mapped in the target sample and the target mark in other samples with these features combined using
       an ensemble of regression trees.

OPTIONS

       Convert
              Converts signal tracks into binned signal resolution tracks.

       ComputeGlobalDist
              Computes the global distance based on correlation for each mark in each sample with the same  mark
              in  all other samples. Creates a file for each mark in each sample containing a ranked list of the
              globally nearest samples.

       GenerateTrainData
              This command takes a directory of converted data and global  distances  and  generates  a  set  of
              training data instances.

       Train  This command trains regression trees based on the feature data produced by GenerateTrainData.

       Apply  This command applies the predictors generated in the Train command to generate the imputed data.

       Eval   Compares the agreement between an observed and imputed data set.

       Version
              Give the version of ChromImpute.

SEE ALSO

       http://www.biolchem.ucla.edu/labs/ernst/ChromImpute/

AUTHOR

       ChromImpute was written by Jason Ernst.

1.0.3                                             December 2017                                   ChromImpute(1)