spillToConvergence: Spillover to convergence

In yxinyi2/ADAPTS1.0.3: Automated Deconvolution Augmentation of Profiles for Tissue Specific Cells

Description

Build an n-pass spillover matrix, continuing until the results converge into clusters of cell types

deconMatrices <- spillToConvergence(sigMatrix, geneExpr, 100, FALSE, TRUE)

Usage

spillToConvergence(
  sigMatrix,
  geneExpr,
  nPasses = 100,
  plotIt = FALSE,
  imputNAs = FALSE,
  method = "DCQ"
)

Arguments

sigMatrix	The deconvolution matrix, e.g. LM22 or MGSM27
geneExpr	The source gene expression matrix used to calculate sigMatrix
nPasses	The maximum number of iterations (DEFAULT: 100)
plotIt	Set to TRUE to plot it (DEFAULT: FALSE)
imputNAs	Set to TRUE to imput genes with missing values & cache the imputed. FALSE will just remove them (DEFAULT: FALSE)
method	One of 'DCQ', 'SVMDECON', 'DeconRNASeq', 'proportionsInAdmixture', 'nnls' (DEFAULT: DCQ)

Value

A list of signature matrices

Examples

#This toy example 
library(ADAPTS)
fullLM22 <- ADAPTS::LM22[1:30, 1:4]
smallLM22 <- fullLM22[1:25,] 

deconMatrices <- spillToConvergence(sigMatrix=smallLM22, geneExpr=fullLM22, nPasses=10, plotIt=TRUE)

yxinyi2/ADAPTS1.0.3 documentation built on Aug. 5, 2020, 12:09 a.m.