RegNMF: Reg Nonnegative Matrix Factorization

In Durenlab/RegNMF: RegNMF

Reg Nonnegative Matrix Factorization

Usage

  RgeNMF(E,
         O,
         Symbol,
         PeakName,
         Symbol_location,
         Peak_location,
         feature_cut_perc=0.01,
         corr_cut_k=100000,
         cell_num_smooth=sqrt(dim(E)[2]),
         core=8)

Arguments

E	matrix or sparseMatrix. Gene by cell matrix.
O	matrix or sparseMatrix. Peak by cell matrix.
Symbol	character. Vector of genes names
PeakName	character Vector of peaks include its location
Symbol_location	character Vector of genes location
Peak_location	characterVector of peaks location
feature_cut_perc	value of filter
corr_cut_k	value of filter
cell_num_smooth	value of filter
core	Number of core to use

Value

W123h$H	H, which is result of RegNMF
W123H$W1	W1, which is result of RegNMF
W123H$W2	W2, which is result of RegNMF
W123H$W3	W3, which is result of RegNMF
W123H$Reg_adj	Regulations of each cell
W123H$Reg_gene_name	target genes of each Reg
W123H$Reg_peak_name	peak_name of each Reg
W123H$Gene_name	Reg_gene_name
W123H$peak_name	Reg_peak_name

Durenlab/RegNMF documentation built on March 19, 2023, 12:27 p.m.