Perform Hierarchical Clustering and tree pruning on samples of VCF file

Performs Hierarchical Clustering on a distance matrix calculated as in vcf2dist and generates a phylogenetic tree (complete linkage by default; single, complete, and average linkage are supported by the Java backend), as in dist2tree. The phylogenetic tree is then pruned with cutreeDynamic to get clusters (as in tree2clusters).

Usage

vcf2clusters(
  inputFile,
  threads = 2,
  cutHeight = NULL,
  minClusterSize = 1,
  extra = TRUE,
  verbose = FALSE
)

Arguments

inputFile

Input vcf file location (uncompressed or gzip compressed).

threads

Number of java threads to use.

cutHeight

Define at which height to cut tree. Default automatically defined.

minClusterSize

Minimum size of clusters. Default 1.

extra

Boolean whether to use extra parameters for the cutreeDynamic.

verbose

Logical. If TRUE, enables verbose output from the Java backend.

Value

A list of :

• dist distances object.

• character vector of the generated phylogenetic tree in Newick format

• character vector of the clusters. Each row contains data for a cluster, separated by space. The id of the cluster, the size of the cluster (number of elements) and the names of its elements, Cluster id 0 contains all the objects not assigned to a cluster (singletons). Example clusters output :

  0	3	Sample1	Sample2	Sample3
  1	3	Sample4	Sample5	Sample6
  2	2	Sample7	Sample8
  3	2	Sample9	Sample0

Details

Biallelic or multiallelic (maximum 7 alternate alleles) SNP and/or INDEL variants are considered, phased or not. Some VCF encoding examples are:

• heterozygous variants : 1/0 or 0/1 or 0/2 or 1|0 or 0|1 or 0|2

• homozygous to the reference allele variants : 0/0 or 0|0

• homozygous to the first alternate allele variants : 1/1 or 1|1

If there are n samples and m variants, an nxn zero-diagonal symmetric distance matrix is calculated. The calculated cosine type distance (1-cosine_similarity)/2 is in the range [0,1] where value 0 means completely identical samples (cosine is 1), value 0.5 means perpendicular samples (cosine is 0) and value 1 means completely opposite samples (cosine is -1).

The calculation is performed by a Java back-end implementation, that supports multi-core CPU utilization and can be demanding in terms of memory resources. By default a JVM is launched with a maximum memory allocation of 512 MB. When this amount is not sufficient, the user needs to reserve additional memory resources, before loading the package, by updating the value of the java.parameters option. For example in order to allocate 4GB of RAM, the user needs to issue options(java.parameters="-Xmx4g") before library(fastreeR).

References

Java implementation: https://github.com/gkanogiannis/BioInfoJava-Utils

Author

Anestis Gkanogiannis, anestis@gkanogiannis.com

Examples

my.clust <- vcf2clusters(
    inputFile = system.file("extdata", "samples.vcf.gz",
        package = "fastreeR"
    )
)
#>  ..cutHeight not given, setting it to 0.0407  ===>  99% of the (truncated) height range in dendro.
#>  ..done.