create_profile_matrix: Create Custom Cell Profile Matrix

In Nanostring-Biostats/SpatialDecon: Deconvolution of mixed cells from spatial and/or bulk gene expression data

Create Custom Cell Profile Matrix

Description

Create custom cell profile matrix using single cell data. The average gene expression for each cell type is returned.

Usage

create_profile_matrix(
  mtx,
  cellAnnots,
  cellTypeCol,
  cellNameCol,
  matrixName = "Custom",
  outDir = "./",
  geneList = NULL,
  normalize = FALSE,
  scalingFactor = 5,
  minCellNum = 15,
  minGenes = 100,
  discardCellTypes = FALSE
)

Arguments

mtx	gene x cell count matrix
cellAnnots	cell annotations with cell type and cell name as columns
cellTypeCol	column containing cell type
cellNameCol	column containing cell ID/name
matrixName	name of final profile matrix
outDir	path to desired output directory, set to NULL if matrix should not be written
geneList	gene list to filter profile matrix to
normalize	Should data be normalized? (TRUE/FALSE) if TRUE data will be normalize using total gene count
scalingFactor	what should all values be multiplied by for final matrix, set to 1 if no scaling is wanted
minCellNum	minimum number of cells of one type needed to create profile, exclusive
minGenes	minimum number of genes expressed in a cell, exclusive
discardCellTypes	should cell types be filtered for types like mitotic, doublet, low quality, unknown, etc.

Value

A custom cell profile matrix genes (rows) by cell types (columns), matrix gets written to disk and outDir

Examples

cellNames <- paste0("Cell", seq_len(1500))
geneNames <- paste0("Gene", seq_len(1500))
mtx <- matrix(data=sample(size = length(cellNames)*length(geneNames),
                          replace = TRUE,
                          x = c(0,seq_len(100)), 
                          prob = c(0.6784, rep(0.0075, 15), rep(0.005, 25),
                                   rep(0.002, 25), rep(0.001, 35))), 
                          ncol = length(cellNames), nrow = length(geneNames), 
                          dimnames = list(geneNames, cellNames))
cellAnnots <- as.data.frame(cbind(CellID=cellNames, 
                                  cellType=sample(size = length(cellNames), 
                                                  replace = TRUE,
                                                  x = c("A", "B", "C", "D"),
                                                  prob = c(0.1, 0.4, 0.3, 0.2))))
table(cellAnnots$cellType)
profile_matrix <- create_profile_matrix(mtx = mtx,    
                                        cellAnnots = cellAnnots, 
                                        cellTypeCol = "cellType",
                                        cellNameCol = "CellID",
                                        minGenes = 10,
                                        scalingFactor = 1)
head(profile_matrix)

Nanostring-Biostats/SpatialDecon documentation built on Jan. 26, 2024, 8:20 p.m.