This function performs a voting scheme to identify cells that are expressing one or multiple genes above a given threshold. The function allows the user to introduce a factor of relaxation in the voting scheme by setting the minimum number of genes that should be coexpressed in a cell for it to be considered. For the obtained set of cells, the function summarizes the expression values of the genes using a user-defined function.
Usage
voting_scheme(
expression_matrix,
genes,
thresh_percentile = 0.25,
thresh_value = 0,
n_coexpressed_thresh = length(genes),
summary_function = NULL
)Arguments
- expression_matrix
The gene by cell expression matrix to be used. The matrix should have defined rownames and colnames.
- genes
A vector with the genes to be used for the voting scheme.
- thresh_percentile
The percentile to be used as threshold for the expression values to select the cells associated with each gene. If set to 0, the threshold will be the value defined in
thresh_value. Defaults to 0.25.- thresh_value
The value to be used as threshold for the expression values to select the cells associated with each gene. Defaults to 0.
- n_coexpressed_thresh
The number of genes that should be coexpressed in a cell for it to be considered as selected. Defaults to the number of provided genes.
- summary_function
A function that takes as argument a numeric vector and summarises it into a single value. If set to NULL, the function will return a factor with the selected cells. Defaults to NULL.