total_sum {HiCcompare} | R Documentation

## 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)

[Package HiCcompare version 1.9.0 Index]