filterSCE {CATALYST} | R Documentation

## `SingleCellExperiment` filtering

### Description

Filters cells/features from a `SingleCellExperiment` using conditional statements a la `dplyr`.

### Usage

    filterSCE(x, ..., k = NULL)

### Arguments

`x` | a `SingleCellExperiment`.
`...` | conditional statements separated by comma. Only rows/columns where the condition evaluates to TRUE are kept.
`k` | numeric or character string. Specifies the clustering to extract populations from. Must be one of `names(cluster_codes(x))`. Defaults to the 1st clustering available.

### Value

a `SingleCellExperiment`.

### Author(s)

Helena L Crowell helena.crowell@uzh.ch

### Examples

    # construct SCE & run clustering
    data(PBMC_fs, PBMC_panel, PBMC_md, merging_table)
    sce <- prepData(PBMC_fs, PBMC_panel, PBMC_md)
    sce <- cluster(sce)

    # one condition only, remove a single sample
    filterSCE(sce, condition == "Ref", sample_id != "Ref1")

    # keep only a subset of clusters
    filterSCE(sce, cluster_id %in% c(7, 8, 18), k = "meta20")

[Package CATALYST version 1.14.1 Index]