total_sum: Total sum normalization for a list of hic.table objects
In HiCcompare: HiCcompare: Joint normalization and comparative analysis of multiple Hi-C datasets
Description
Usage
Arguments
Details
Value
Examples
Description
Total sum normalization for a list of hic.table objects
Usage
1
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
1
2
3
4
5
6
7
8
9
10
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)
HiCcompare documentation built on Nov. 8, 2020, 8:26 p.m.
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Description Usage Arguments Details Value Examples
Description
Total sum normalization for a list of hic.table objects
Usage
1 | 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
1 2 3 4 5 6 7 8 9 10 | 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)
|
R Package Documentation
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We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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