construct_genotype_cluster_graph: construct_genotype_cluster_graph

In bjstewart1/GenotypeMixtures: Get donors from a set of souporcell outputs and an experimental design

construct_genotype_cluster_graph

Description

Function that constructs a genotype cluster graph using a set of SOC directories and an experimental design

Usage

construct_genotype_cluster_graph(
  experimental_design,
  file_locations,
  ncounts = 10,
  use_VAF = TRUE
)

Arguments

experimental_design	an experimental design matrix rownames should be microfluidics channels, colnames should be genotypes
file_locations	the file locations
ncounts	numeric - the number of counts supporting each variant
use_VAF	if TRUE calculates genotype to genotype similarity on the basis of mean squared error between variant allele frequencies, if FALSE calculates relatedness (Pedersen et al. 2020) using a reimplementation of the Somalier approach.

Value

a list $graph_membership gives you cluster memberships $graph_plot gives a force directed embedding of the graph $membership_plot gives a heatmap of memberships $membership_matrix gives a matrix of channel memberships

Examples

construct_genotype_cluster_graph()

bjstewart1/GenotypeMixtures documentation built on Aug. 27, 2022, 2:01 p.m.