snv.clustering: Cluster samples based on SNVs.

Description Usage Arguments Details Value Author(s) Examples

Description

Perform hierarchical clustering of samples based on their somatic SNVs.

Usage

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

Arguments

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.

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.

Value

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

Author(s)

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

Examples

1
2
3
4
5
6
7
8
9
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')

jjellis/GenomicVis documentation built on May 19, 2019, 11:39 a.m.