Package index • metabinR

Binning functions

High-level entry points for metagenome binning.

abundance_based_binning(): Abundance based binning on metagenomic samples
composition_based_binning(): Composition based binning on metagenomic samples
hierarchical_binning(): Hierarchical (ABxCB) binning on metagenomic samples

Result analysis

Summarize assignments and compare them with known read origins.

bin_summary(): Summarize the bins in a metabinR result
ambiguous_reads(): Find reads with close competing bins
evaluate_bins(): Evaluate read-level bin assignments against known origins

MetabinResult

S4 container for binning assignments and parameters.

show(<MetabinResult>): MetabinResult: binning result container
assignments() nClusters() parameters() algorithm(): Accessors for MetabinResult
as.data.frame(<MetabinResult>): Convert a MetabinResult to a data.frame

JVM configuration

metabinR_jvm_options(): JVM options used when metabinR loads