filter_genes {ccfindR} | R Documentation |
Select genes with high relative variance in count data for further analysis
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)
object |
|
markers |
A vector containing marker genes to be selected.
All rows in
|
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 |
For a very large number of cells, calculate VMR
row by row while avoiding calls to |
plot |
Plot the distribution of no. of cells expressed vs. VMR. |
log |
Axis in log-scale, |
cex |
Symbol size for each gene in the plot. |
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.
Object of class scNMFSet
.
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)