choose_features_clustering: choose_features_clustering

In MitoHEAR: Quantification of Mitochondrial DNA Heteroplasmy

choose_features_clustering

Description

choose_features_clustering

Usage

choose_features_clustering(
  heteroplasmy_matrix,
  allele_matrix,
  cluster,
  top_pos,
  deepSplit_param,
  minClusterSize_param,
  min_value_vector,
  threshold = 0.2,
  index,
  max_frac = 0.7
)

Arguments

heteroplasmy_matrix	Third element returned by get_heteroplasmy.
allele_matrix	Fourth element returned by get_heteroplasmy.
cluster	Vector specifying a partition of the samples.
top_pos	Numeric value. Number of bases sorted with decreasing values of distance variance (see section Details below) among samples. If relevant_bases=NULL, then the bases for performing hierarchical clustering are the ones whose relative variance (variance of the base divided sum of variance among top_pos bases) is above min_value.
deepSplit_param	Integer value between 0 and 4 for the deepSplit parameter of the function cutreeHybrid. See section Details below.
minClusterSize_param	Integer value specifying the minClusterSize parameter of the function cutreeHybrid. See section Details below.
min_value_vector	Numeric vector. For each value in the vector, the function clustering_angular_distance is run with parameter min_value equal to one element of the vector min_value_vector.
threshold	Numeric value. If a base has heteroplasmy greater or equal to threshold in more than max_frac of cells, then the base is not considered for down stream analysis.
index	Fifth element returned by get_heteroplasmy.
max_frac	Numeric value.If a base has heteroplasmy greater or equal to threshold in more than max_frac of cells, then the base is not considered for down stream analysis.

Value

Clustree plot returned by function clustree from package clustree.

Author(s)

Gabriele Lubatti [e-mail]

See Also

https://cran.r-project.org/package=clustree

MitoHEAR documentation built on March 18, 2022, 6:47 p.m.