select_genes: Select features based on mean expression and variance

In scfurl/seqGlue: Makes sequencing data come together like glue

Select features based on mean expression and variance

Description

Many genes typically co-vary with one another, and so the dimensionality of the data can be reduced with a wide variety of different algorithms. After calculating dispersion for a using the calc_dispersion function, the select_genes function allows the user to identify a set of genes that will be used in downstream dimensionality reduction methods.

Usage

select_genes(
  obj,
  fit_min = 1,
  fit_max = Inf,
  logmean_ul = Inf,
  logmean_ll = -Inf,
  top_n = NULL
)

Arguments

obj	the output of the calc_dispersion function.
fit_min	the minimum multiple of the dispersion fit calculation; default = 1
fit_max	the maximum multiple of the dispersion fit calculation; default = Inf
logmean_ul	the maximum multiple of the dispersion fit calculation; default = Inf
logmean_ll	the maximum multiple of the dispersion fit calculation; default = Inf
top	top_n if specified, will override the fit_min and fit_max to select the top n most variant features. logmena_ul and logmean_ll can still be used.

Value

an updated object (list) that records the selected features

scfurl/seqGlue documentation built on Sept. 1, 2024, 11:20 a.m.