HiCociety (version 0.1.38)

ConnectivityDiff: Connectivity difference between two conditions

Description

output table of connectivity difference of modules between cell types is generated.

Usage

ConnectivityDiff(wt, ko, prefix.wt, prefix.ko, resolution = 5000)

Value

A list of two data.frame objects, each representing the network connectivity differences of modules in condition 1 or condition 2 when compared to the counterpart cell type. Each data.frame contains the following columns: "chr", "module_start", "module_end", "connectivity", "transitivity", "centrality_node", "idx" (the row index of the module in the input module object), "connectivity_in_(counterpart_cell_type)", "connectivity_difference", and "connectivity_foldchange".

Arguments

wt

hic2community result from condition 1

ko

hic2community result from condition 2

prefix.wt

Prefix for wt to be presented in the column names

prefix.ko

Prefix for ko to be presented in the column names

resolution

Resolution of Hi-C dataset

Author

Sora Yoon, PhD

Details

Connectivity difference between two conditions

Examples

modulefile1 = system.file('extdata','mouse_naiveCD4T_Vahedi_short.rds',
package = 'HiCocietyExample')
modulefile2 = system.file('extdata','mouse_Th1_Vahedi_short.rds',
package = 'HiCocietyExample')
mycom1 = readRDS(modulefile1)
mycom2 = readRDS(modulefile2)
result = ConnectivityDiff(mycom1, mycom2, 'NaiveCD4T', 'Th1',
resolution = 5000)
head(print(result))