filter_genes {ccfindR} | R Documentation

## Filter genes with quality control criteria

### Description

Select genes with high relative variance in count data for further analysis

### Usage

    filter_genes(object, markers = NULL, vmr.min = 0,
      min.cells.expressed = 0, max.cells.expressed = Inf,
      rescue.genes = FALSE, progress.bar = TRUE, save.memory = FALSE,
      plot = TRUE, log = "xy", cex = 0.5)

### Arguments

`object` | `scNMFSet` object.
`markers` | A vector containing marker genes to be selected. All rows in `rowData` that contain columns matching this set will be selected.
`vmr.min` | Minimum variance-to-mean ratio for gene filtering.
`min.cells.expressed` | Minimum no. of cells expressed for gene filtering.
`max.cells.expressed` | Maximum no. of cells expressed for gene filtering.
`rescue.genes` | Selected additional genes whose (non-zero) count distributions have at least one mode.
`progress.bar` | Display progress of mode-gene scan or VMR calculation with `save.memory = TRUE`.
`save.memory` | For a very large number of cells, calculate VMR row by row while avoiding calls to `as.matrix()`. Progress bar will be displayed unless `progress.bar=FALSE`.
`plot` | Plot the distribution of no. of cells expressed vs. VMR.
`log` | Axis in log-scale, `c('x','y','xy')`.
`cex` | Symbol size for each gene in the plot.

### Details

Takes as input `scNMFSet` object and scatterplot no. of cells expressed versus VMR (variance-to-mean ratio) for each gene. Optionally, genes are filtered using minimum VMR together with a range of no. of cells expressed.

### Value

Object of class `scNMFSet`.

### Examples

    set.seed(1)
    s <- scNMFSet(matrix(stats::rpois(n=1200,lambda=3),40,30))
    s <- filter_genes(s,vmr.min=1.0,min.cells.expressed=28,
            rescue.genes=FALSE)

[Package ccfindR version 1.7.0 Index]