attractorFinding: Find all co-expressed signatures in the expression matrix

In zky0708/2DImpute: 2DImpute: Imputing scRNA-seq data from correlations in both dimensions

Description

This function uses heuristic exhaustive search to find existing co-expressed signatures in the expression matrix, with attractor finding algorithm implemented in the R package cafr.

Usage

attractorFinding(
  exprs,
  genes_involved = NULL,
  a = 5,
  epsilon = 1e-04,
  mi_threshold = 0.4,
  verbose = TRUE
)

Arguments

exprs	A log-transformed expression data matrix of which rows and columns represent genes and cells, respectively.
genes_involved	A vector containing genes that will be used as seeds in the attractor finding process. Default is NULL, in which case all genes in the expression matrix will be used.
a	Exponent of mutual information (MI) used to create weighted vector for metagenes, one of parameters in function findAttractor in package cafr. Default is 5.
epsilon	Convergence threshold, one of parameters in function findAttractor in package cafr. Default is 1E-4.
mi_threshold	MI threshold (between 0 to 1) to determine the gene membership of signatures. Genes with greater than or equal to the threshold are considered to be associated with the signature. Default is 0.4.
verbose	Whether to show the finding progress. Default is TRUE.

Value

An attractor list in which each element contains the vector of MIs between the genes and the converged metagene for each attractor signature.

Examples

data(ge_10x_sample)
attractors <- attractorFinding(exprs = ge_10x_sample, genes_involved = c('CD3D', 'XIST'))

zky0708/2DImpute documentation built on March 12, 2020, 3:13 a.m.