cellTypeEstimate | R Documentation |
Primary function for cell type profile estimations.
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)
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 |
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