buildSpilloverMat: Build a spillover matrix

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

Description

Build a spillover matrix, i.e. what do purified samples deconvolve as?

spillExpr <- buildSpilloverMat(refExpr, geneExpr, method='DCQ')

Usage

buildSpilloverMat(refExpr, geneExpr, method = "DCQ")

Arguments

refExpr	The deconvolution matrix, e.g. LM22 or MGSM27
geneExpr	The full gene expression for purified cell types. Multiple columns (examples) for each column in the reference expr.
method	One of 'DCQ', 'SVMDECON', 'DeconRNASeq', 'proportionsInAdmixture', 'nnls' (DEFAULT: DCQ)

Value

A spillover matrix showing how purified cell types deconvolve

Examples

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

spillover <- buildSpilloverMat(refExpr=smallLM22, geneExpr=fullLM22, method='DCQ')

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