remakeLM22p {ADAPTS}

Make an Augmented Signature Matrix

Description

With the ADAPTSdata packge, it will use the full LM22 data matrix and add a few additional genes to cover osteoblasts, osteoclasts, Plasma.memory, MM. In many ways this is just a convenient wrapper for AugmentSigMatrix that calculates and caches a gList.

Usage

remakeLM22p(
  exprData,
  fullLM22,
  smallLM22 = NULL,
  plotToPDF = TRUE,
  condTol = 1.01,
  postNorm = TRUE,
  autoDetectMin = FALSE,
  pdfDir = tempdir(),
  oneCore = FALSE,
  cache_gList = TRUE
)

Arguments

exprData

The gene express data to use to augment LM22, e.g. ADAPTSdata::addMGSM27

fullLM22

LM22 data with all genes. Available in ADAPTSdata2::fullLM22

smallLM22

The small LM22 matrix, if it includes new cell types in exprData those will not be overwritten (DEFAULT: NULL, i.e. buildLM22plus(useLM22genes = TRUE)

plotToPDF

TRUE: pdf, FALSE: standard display (DEFAULT: TRUE)

condTol

The tolerance in the reconstruction algorithm. 1.0 = no tolerance, 1.05 = 5% tolerance (DEFAULT: 1.01)

postNorm

Set to TRUE to normalize new signatures to match old signatures. To Do: Redo Kappa curve? (DEFAULT: TRUE)

autoDetectMin

Set to true to automatically detect the first local minima. GOOD PRELIMINARY RESULTS (DEAFULT: FALSE)

pdfDir

A fold to write the pdf file to if plotToPDF=TRUE (DEFAULT: tempdir())

oneCore

Set to TRUE to disable parallelization (DEFAULT: FALSE)

cache_gList

Set to TRUE to cache slow gList calculations (DEFAULT: TRUE)

Value

a cell type signature matrix

Examples

#This toy example treats the LM22 deconvolution matrix as if it were all of the data
#  For a real example, look at the vignette or comments in exprData, fullLM22, small LM22
library(ADAPTS)
fullLM22 <- ADAPTS::LM22[1:200, 1:8]
#Make a fake signature matrix out of 100 genes and the first 8 cell types
smallLM22 <- fullLM22[1:100, 1:8] 

#Make fake data representing two replicates of purified Mast.cells types 
exprData <- ADAPTS::LM22[1:200, c("Mast.cells.resting","Mast.cells.activated")]
colnames(exprData) <- c("Mast.cells", "Mast.cells")
newSig <- remakeLM22p(exprData=exprData, fullLM22=fullLM22, smallLM22=smallLM22, 
    plotToPDF=FALSE, oneCore=TRUE, cache_gList=FALSE)