estimateGeneProgramsFabia: Estimate Gene Programs with FABIA

In kharchenkolab/cacoa: Case-Control Analysis Tools for Single-Cell RNA-Seq

Estimate Gene Programs with FABIA

Description

Estimate Gene Programs with FABIA

Usage

estimateGeneProgramsFabia(
  z.scores,
  n.programs,
  n.sampled.cells = 15000,
  cyc = 1500,
  alpha = 0.2,
  random = -1,
  ...
)

Arguments

n.programs	maximal number of gene programs to find (parameter p for fabia).
n.sampled.cells	number of sub-sampled cells for estimating the gene programs. If 0, all cells are used. it is interpreted as a vector of cell
...	Arguments passed on to fabia::fabia spl sparseness prior loadings (0 - 2.0); default = 0 (Laplace). spz sparseness factors (0.5 - 2.0); default = 0.5 (Laplace). non_negative Non-negative factors and loadings if non_negative > 0; default = 0. center data centering: 1 (mean), 2 (median), > 2 (mode), 0 (no); default = 2. norm data normalization: 1 (0.75-0.25 quantile), >1 (var=1), 0 (no); default = 1. scale loading vectors are scaled in each iteration to the given variance. 0.0 indicates non scaling; default = 0.0. lap minimal value of the variational parameter; default = 1.0 nL maximal number of biclusters at which a row element can participate; default = 0 (no limit) lL maximal number of row elements per bicluster; default = 0 (no limit) bL cycle at which the nL or lL maximum starts; default = 0 (start at the beginning)

kharchenkolab/cacoa documentation built on Nov. 8, 2024, 6:06 a.m.