get.references.apcluster: get.references.apcluster

In ttdtrang/gbnorm: Graph-based Normalization of RNA-seq data

Description

Graph-based identify the set of references using affinity propagation as the underlying clustering method

Usage

get.references.apcluster(
  m,
  cor.method = "pearson",
  min.size = 10,
  min.corr = 0.75,
  min.count = 0,
  med.quantile = 0.5,
  log.base = 2,
  debug = FALSE,
  verbose.output = FALSE,
  ...
)

Arguments

m	expression matrix, genes x samples (which will be transposed internally)
cor.method	[="pearson"] the correlation method used to construct edges between genes. Acceptable values are same as those of R base function 'cor()'.
min.size	minimum size of the candidate refernece clusters
min.count	minimum count of a gene across all samples, for it to be retained in constructing the graph
med.quantile	the quantile above which a gene should be expressed in all samples, for it to be retained in constructing the graph
log.base	the base to log-transform the expression matrix
debug	whether to print additional information when running
verbose.output	whether to all clusters (in addition to the reference one) in the output

ttdtrang/gbnorm documentation built on Dec. 23, 2021, 1:01 p.m.