SiFINeT (version 1.13)

SiFINeT-class: The SiFINeT Class

Description

The SiFINeT Class

Slots

data

a list of cell (row) by gene (column) count matrix, either regular or sparse matrix

sparse

whether the count matrix should be analyzed as sparse matrix

meta.data

matrix of meta data, the number of rows should equal to the number of cells

gene.name

a vector of names of genes with length equal to the number of genes

data.name

name of the dataset

n

number of cells in the dataset

p

number of genes in the dataset

data.thres

binarized count matrix

coexp

matrix of genes coexpression

est_ms

estimated mean and sd of coexpression values

thres

lower bound of coexpression (or absolute value of coexpression) for network edge assignment

q5

50% quantile for each gene

kset

index of kept genes after the filtering step

conn

list of connectivities in absolute network

conn2

list of connectivities in positive sub-network

fg_id

index of the candidate feature genes

uni_fg_id

index of the candidate unique feature genes

uni_cluster

cluster result of the candidate unique feature genes

selected_cluster

selected unique feature gene clusters

featureset

detected set of feature genes