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Composition based binning on metagenomic samples

Source: R/composition_based_binning.R
composition_based_binning.Rd

This function performs composition based binning on metagenomic samples, directly from FASTA or FASTQ files, by short kmer analysis (k<8). See doi:10.1186/s12859-016-1186-3 for more details.

Usage

composition_based_binning(
  ...,
  kMerSizeCB = 4,
  numOfClustersCB = 5,
  outputCB = "CB.cluster",
  keepQuality = FALSE,
  dryRun = FALSE,
  gzip = FALSE,
  numOfThreads = BiocParallel::bpworkers()
)

Arguments

...

Input sequences. Either character paths to FASTA/FASTQ files (uncompressed or gzip compressed), a DNAStringSet / QualityScaledDNAStringSet, or a ShortReadQ object. Non-file inputs are staged to a temporary FASTA/FASTQ file for the Java backend.

kMerSizeCB

kmer length for Composition based Binning.

numOfClustersCB

Number of Clusters for Composition based Binning.

outputCB

Output Composition based Binning Clusters files location and prefix.

keepQuality

Keep fastq qualities on the output files. (will produce .fastq)

dryRun

Don't write any output files.

gzip

Gzip output files.

numOfThreads

Number of threads to use. Defaults to bpworkers().

Value

A MetabinResult object. Its assignments slot is a DataFrame with numOfClustersCB + 2 columns:

  • read_id : read identifier from fasta header

  • CB : read was assigned to this CB cluster index

  • CB.n : read to cluster CB.n distance

For backwards-compatible data.frame output use as.data.frame(result).

References

https://github.com/gkanogiannis/metabinR

Author

Anestis Gkanogiannis, anestis@gkanogiannis.com

Examples

res <- composition_based_binning(
    system.file("extdata", "reads.metagenome.fasta.gz", package = "metabinR"),
    dryRun = TRUE, kMerSizeCB = 2
)
res
#> MetabinResult (CB)
#>   reads:     26,664
#>   clusters:  5
#>   inputs:    1 file(s)
#>     - /home/runner/work/_temp/Library/metabinR/extdata/reads.metagenome.fasta.gz