getPart {FateID} | R Documentation |
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 |
fthr |
vector of real positive numbers. This vector has to have the same length as the list |
n |
positive integer number. For each component of |
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 |
thr |
A vector with expression threshold values applied for each component in the 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)