total_sum: Total sum normalization for a list of hic.table objects

In dozmorovlab/HiCcompare: HiCcompare: Joint normalization and comparative analysis of multiple Hi-C datasets

Total sum normalization for a list of hic.table objects

Description

Total sum normalization for a list of hic.table objects

Usage

total_sum(hic.list)

Arguments

hic.list

A list of hic.table objects created by the create.hic.table function. When creating the hic.list to be entered into this function you must set the scale option to FALSE.

Details

This function will scale the IFs based on the total sum of the counts for the genome instead of on a per chromosome basis as done in the create.hic.table function when the scale option is set to TRUE. The idea behind this function to preserve more local CNV differences while still accounting for technical biases which can cause the total read counts to differ between sequencing runs.

Value

A list of hic.table objects.

Examples

data('HMEC.chr22')
data('NHEK.chr22')
data('HMEC.chr10')
data('NHEK.chr10')
hic.table1 <- create.hic.table(HMEC.chr22, NHEK.chr22,
    chr = 'chr22', scale = FALSE)
hic.table2 <- create.hic.table(HMEC.chr10, NHEK.chr10,
    chr = 'chr10', scale = FALSE)
hic.list <- list(hic.table1, hic.table2)
scaled_list <- total_sum(hic.list)

dozmorovlab/HiCcompare documentation built on June 30, 2023, 3:09 a.m.