filterTrajFeaturesByFF {CellTrails} | R Documentation

## Filter features by Fano Factor

### Description

Filters trajectory features that exhibit a significantly high fano factor (index of dispersion) by considering average expression levels.

### Usage

    filterTrajFeaturesByFF(
      sce,
      threshold = 1.7,
      min_expr = 0,
      design = NULL,
      show_plot = TRUE
    )

### Arguments

`sce` | An `SingleCellExperiment` object
`threshold` | A Z-score cutoff (default: 1.7)
`min_expr` | Minimum average expression of feature to be considered
`design` | A numeric matrix describing the factors that should be blocked
`show_plot` | Indicates if plot should be shown (default: TRUE)

### Details

To identify the most variable features an unsupervised strategy that controls for the relationship between a features’s average expression intensity and its expression variability is applied. Features are placed into 20 bins based on their mean expression. For each bin the fano factor (a windowed version of the index of dispersion, IOD = variance / mean) distribution is computed and standardized (Z-score(x) = x/sd(x) - mean(x)/sd(x)). Features with a Z-score greater than `threshold` remain labeled as trajectory feature in the `SingleCellExperiment` object. The parameter `min_expr` defines the minimum average expression level of a feature to be considered for this filter method. Please note that spike-in controls are ignored and are not listed as trajectory features.
To account for systematic bias in the expression data (e.g., cell cycle effects), a design matrix can be provided for the learning process. It should list the factors that should be blocked and their values per sample. It is suggested to construct a design matrix with `model.matrix`.

### Value

A `character` vector

### Author(s)

Daniel C. Ellwanger

### See Also

`trajFeatureNames` `model.matrix`

### Examples

    # Simulate example data
    set.seed(1101)
    dat <- simulate_exprs(n_features=15000, n_samples=100)

    # Create container
    alist <- list(logcounts=dat)
    sce <- SingleCellExperiment(assays=alist)

    # Filter incrementally
    trajFeatureNames(sce) <- filterTrajFeaturesByDL(sce, threshold=2)
    trajFeatureNames(sce) <- filterTrajFeaturesByCOV(sce, threshold=0.5)
    trajFeatureNames(sce) <- filterTrajFeaturesByFF(sce, threshold=1.7)

    # Number of features
    length(trajFeatureNames(sce)) #filtered
    nrow(sce) #total

[Package CellTrails version 1.12.0 Index]