construct_genotype_cluster_graph

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

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

# \donttest{
construct_genotype_cluster_graph()
#> Error in construct_genotype_cluster_graph(): argument "file_locations" is missing, with no default
# }