filter_correlated_cell_scExp {ChromSCape} | R Documentation

## Filter lowly correlated cells

### Description

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

### Usage

    filter_correlated_cell_scExp(scExp, random_iter = 5,
    corr_threshold = 99, percent_correlation = 1,
    downsample = 2500, verbose = TRUE, n_process = 250,
    BPPARAM = BiocParallel::bpparam())

### Arguments

`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)
`downsample` | Number of cells to calculate correlation filtering threshold ? (2500)
`verbose` | Print messages ? (TRUE)
`n_process` | Number of cell to proceed at a time. Increase this number to increase speed at memory cost
`BPPARAM` | BPPARAM object for multiprocessing. See bpparam for more informations. Will take the default BPPARAM set in your R session.

### Details

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.

### Value

Returns a SingleCellExperiment object without lowly correlated cells. The calculated correlation score limit threshold is saved in metadata.

### Examples

    data("scExp")
    dim(scExp)
    scExp_cf = filter_correlated_cell_scExp(scExp,
    corr_threshold = 99, percent_correlation = 1)
    dim(scExp_cf)

[Package ChromSCape version 1.2.62 Index]