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 = TRUE, progress.bar = TRUE,
  save.memory = FALSE, plot = TRUE, 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.

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 1.0.0 Index]