filter_correlated_cell_scExp {ChromSCape} | R Documentation |
Remove cells that have a correlation score lower than what would be expected by chance with other cells.
filter_correlated_cell_scExp( scExp, random_iter = 50, corr_threshold = 99, percent_correlation = 1, run_tsne = FALSE, verbose = FALSE )
scExp |
A SingleCellExperiment object containing 'Cor', a correlation matrix, in reducedDims. |
random_iter |
Number of random matrices to create to calculate random correlation scores. (50) |
corr_threshold |
Quantile of random correlation score above which a cell is considered to be 'correlated' with another cell. (99) |
percent_correlation |
Percentage of the cells that any cell must be 'correlated' to in order to not be filtered. (1) |
run_tsne |
Re-run tsne ? (FALSE) |
verbose |
(TRUE) |
This functions takes as input a SingleCellExperiment object that must have correlation matrix calculated and outputs a SingleCellExperiment object without lowly correlated cells. TSNE is recalculated.
Returns a SingleCellExperiment object without lowly correlated cells. The calculated correlation score limit threshold is saved in metadata.
data("scExp") dim(scExp) scExp_cf = filter_correlated_cell_scExp(scExp, corr_threshold = 99, percent_correlation = 1) dim(scExp_cf)