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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.
AUTHOR¶
ChromImpute was written by Jason Ernst.
