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.