sclink_norm {scLink}

Pre-process data for scLink

Description

Pre-process data for scLink

Usage

sclink_norm(
  count,
  scale.factor = 1e+06,
  filter.genes = FALSE,
  gene.names = NULL,
  n = 500
)

Arguments

count

A full gene count matrix with rows representing cells and columns representing genes. Gene names are given as column names.

scale.factor

A number specifying the sclae factor used for library size normalization. Defaults to 1e6.

filter.genes

A Boolean specifying whether scLink should select genes based on mean expression. When set to FALSE, users need to speicfy a set of genes to be used for network construction with gene.names. When set to TRUE, scLink will select genes based on their mean expression, and users need to specify the number of genes to be selected with n.

gene.names

A character vector specifying the genes used for network construction. Only needed when filter.genes = FALSE.

n

An integer specifying the number of genes to be selected by scLink (defaults to 500). Only needed when filter.genes = TRUE.

Value

A transformed and normalized gene expression matrix that can be used for correlation calculation and network construction.

Author(s)

Wei Vivian Li, [e-mail]

Examples

count = readRDS(system.file("extdata", "example.rds", package = "scLink"))
count.norm = sclink_norm(count, scale.factor = 1e6, filter.genes = TRUE, n = 500)