gene.vs.molecule.cell.filter {pagoda2}

Filter cells based on gene/molecule dependency

Description

Filter cells based on gene/molecule dependency

Usage

gene.vs.molecule.cell.filter(
  countMatrix,
  min.cell.size = 500,
  max.cell.size = 50000,
  p.level = min(0.001, 1/ncol(countMatrix)),
  alpha = 0.1,
  plot = TRUE,
  do.par = TRUE
)

Arguments

countMatrix

input count matrix to be filtered

min.cell.size

numeric Min allowed cell size (default=500)

max.cell.size

numeric Max allowed cell size (default=5e4)

p.level

numeric Statistical confidence level for deviation from the main trend, used for cell filtering (default=min(1e-3,1/ncol(countMatrix)))

alpha

numeric Shading of the confidence band (default=0.1)

plot

boolean Plot the molecule distribution and the gene/molecule dependency fit (default=TRUE)

do.par

boolean Reset graphical parameters prior to plotting (default=TRUE)

Value

a filtered matrix