Description Usage Arguments Details Value Examples

View source: R/correlation_filtering_clustering.R

Remove cells that have a correlation score lower than what would be expected by chance with other cells.

1 2 3 4 5 6 7 8 | ```
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.

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