ADAPTS (version 0.9.21)

hierarchicalClassify: Build clusters based on n-pass spillover matrix

Description

Build clusters based on n-pass spillover matrix

Usage

hierarchicalClassify(sigMatrix, geneExpr, toPred, hierarchData = NULL,
  pdfDir = tempdir(), oneCore = FALSE, nPasses = 100,
  remZinf = TRUE)

Arguments

sigMatrix

The deconvolution matrix, e.g. LM22 or MGSM27

geneExpr

The source gene expression matrix used to calculate sigMatrix

toPred

The gene expression to ultimately deconvolve

hierarchData

The results of hierarchicalSplit OR hierarchicalSplit.sc (DEFAULT: NULL, ie hierarchicalSplit)

pdfDir

A fold to write the pdf file to (DEFAULT: tempdir())

oneCore

Set to TRUE to disable parallelization (DEFAULT: FALSE)

nPasses

The maximum number of iterations for spillToConvergence (DEFAULT: 100)

remZinf

Set to TRUE to remove any ratio with zero or infinity when generating gList (DEFAULT: FALSE)

Value

a matrix of cell counts

Examples

# NOT RUN {
#This toy example 
library(ADAPTS)
fullLM22 <- ADAPTS::LM22[1:30, 1:4]
smallLM22 <- fullLM22[1:25,] 

cellCounts <- hierarchicalClassify(sigMatrix=smallLM22, geneExpr=fullLM22, toPred=fullLM22, 
    oneCore=TRUE, nPasses=10)
# }