snv.clustering: Cluster samples based on SNVs.
In jjellis/GenomicVis: Genomic Visualisation Routines

Description Usage Arguments Details Value Author(s) Examples

Perform hierarchical clustering of samples based on their somatic SNVs.

1	snv.clustering(vcf.files, genome, sample.names = NULL, ...)

`vcf.files`	A character vector containing the paths to the VCF files to process.
`genome`	A character string identifying the genome
`sample.names`	A character vector of samples names corresponding to each VCF file, by default the file names of the VCFs will be used as sample names.
`...`	Additional parameters pass to `read.vcf`. These can be used to apply additional filtering of the SNVs, see the documentation of `read.vcf` for further details.

Each vcf file should contain called somatic SNVs. use exclude.filtered = TRUE (the default) to only use SNVs with 'PASS' or '.' in the FILTER column.

Invisible returns an object of class hclust that describes the tree produced by the clustering process.

Jonathan Ellis <jonathan.j.ellis@gmail.com>

vcf.files <- c(
  system.file('extdata', 'LC1_TUMOUR_A.vcf', package = 'GenomicVis'),
  system.file('extdata', 'LC1_TUMOUR_B.vcf', package = 'GenomicVis'),
  system.file('extdata', 'LC2_TUMOUR_A.vcf', package = 'GenomicVis'),
  system.file('extdata', 'LC2_TUMOUR_B.vcf', package = 'GenomicVis'),
  system.file('extdata', 'LC3_TUMOUR_A.vcf', package = 'GenomicVis'),
  system.file('extdata', 'LC3_TUMOUR_B.vcf', package = 'GenomicVis'))
sample.names <- tools::file_path_sans_ext(basename(vcf.files))
snv.clustering(vcf.files, sample.names, genome = 'hg19')