cellTypeEstimate: Calculate cell type profile estimations

In oganm/brainGenesManuscript: Marker genes of brain cell types and their use in analysis of whole tissue data

Calculate cell type profile estimations

Description

Primary function for cell type profile estimations.

Usage

cellTypeEstimate(exprData, genes, geneColName = "Gene.Symbol",
  outlierSampleRemove = FALSE, synonymTaxID = NULL,
  geneTransform = function(x) {     mouse2human(x)$humanGene }, groups,
  tableOut = NULL, indivGenePlot = NULL, seekConsensus = F,
  removeNegatives = TRUE, plotType = c("groupBased", "cummulative"),
  PC = 1)

Arguments

exprData	data.frame. Expression data. First collumns of the expression data should include gene names in the same format as the ones specified in the marker gene lists. Any other non-expression related fields must not be of type 'double'
genes	a named list containing marker gene lists of each cell type
geneColName	character. name of the column containing the gene names in the expression file
outlierSampleRemove	logical. should the outlier samples be removed from the final output
synonymTaxID	Taxonomy identifier of the source of cell type markers. If provided, synonyms of the genes will be added as markers, not recommended since unrelated genes can share names
geneTransform	a function that will be applied to the gene list. the default behavior is to change mouse genes to human genes. set to NULL to keep the genes as they are
groups	a vector stating which groups each sample belongs to
tableOut	character, filename. If provided outputs loadings of individual genes and variance explained by principal components
indivGenePlot	a character vector. If provided, plots expression of marker genes in individual groups per marker gene list. Is not guaranteed to look pretty.
seekConsensus	logical. If TRUE any gene with negative loadings in any of the groups individually will be removed. Use if there is a high likelihood of gene regulation between the groups.
removeNegatives	logical. should the genes with negative loadings be removed from the estimation. Setting seekConsensus to TRUE makes this irrelevant. As all negatives will be removed at that step
plotType	if indivGenePlot is provided, type of plot to be saved. groupBased separates expression between groups cummulative plots a single value
PC	which principal component to use. For debugging purposes. Recommended value is always 1

oganm/brainGenesManuscript documentation built on Aug. 24, 2022, 7:48 p.m.