getPart {FateID}

Inference of a cell type partition

Description

This function performs an inference of a cell type partition based on the expression of marker genes.

Usage

getPart(x, FMarker, fthr = NULL, n = 25)

Arguments

x

expression data frame with genes as rows and cells as columns. Gene IDs should be given as row names and cell IDs should be given as column names. This can be a reduced expression table only including the features (genes) to be used in the analysis.

FMarker

list of vectors of gene IDs corresponding to valid rownames of x. The gene IDs within each component of FMarker are considered as marker genes of one of the cell types in the dataset. The aggregated expression of the genes for each component is compared to a threshold defined by the input argument fthr or n. All cells exceeding this threshold are assigned to a cluster representing cells with expression of the respective marker genes.

fthr

vector of real positive numbers. This vector has to have the same length as the list FMarker and contains a threshold for the aggregated expression of all genes in the corresponding component of FMarker. If NULL then a threshold is inferred from the n top-expressing cells for the genes in the respective component of FMarker.

n

positive integer number. For each component of FMarker the expression of all genes is aggregated in every cell and the n top-expressing cells are extracted. The average expression across these cell defines the expression threshold applied to infer the partitioning. Default value is 25.

Value

A list with the following three components:

part

A vector with a partitioning, i. e. cluster assignment for each cell.

tar

A vector with the numbers of target clusters. Cluster 1 comprises all cells with no enrichment of marker genes. The remaining clusters correspond to cell types up-regulating the markers in the list FMarker in the same order as in this list.

thr

A vector with expression threshold values applied for each component in the list FMarker in the same order as in this list.

Examples

x <- intestine$x
y <- intestine$y

FMarker <- list(c("Defa20__chr8","Defa24__chr8"), "Clca3__chr3", "Alpi__chr1")
xf <- getPart(x,FMarker,fthr=NULL,n=5)