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.TH ChromImpute 1 "December 2017" "1.0.3"
.SH NAME
ChromImpute \- Large-scale systematic epigenome imputation
.SH SYNOPSIS
\fBjava -Xmx[GB]g -jar /usr/share/java/chromimpute.jar\fR [\fIoptions\fR]
.SH 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. 
.SH OPTIONS
.TP
\fBConvert
Converts signal tracks into binned signal resolution tracks.
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.TP
\fBComputeGlobalDist
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.
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.TP
\fBGenerateTrainData
This command takes a directory of converted data and global distances and
generates a set of training data instances.
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.TP
\fBTrain
This command trains regression trees based on the feature data produced by
GenerateTrainData.
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.TP
\fBApply
This command applies the predictors generated in the Train command to generate the
imputed data.
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.TP
\fBEval
Compares the agreement between an observed and imputed data set.
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.TP
\fBVersion
Give the version of ChromImpute.
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.SH SEE ALSO
.BR http://www.biolchem.ucla.edu/labs/ernst/ChromImpute/
.SH AUTHOR
ChromImpute was written by Jason Ernst.