depth.adj: Sequencing depth adjustment

In MonkeyLB/hicrep: Measuring the reproducibility of Hi-C data

Description

Sequencing depth could be a confounding effect when measuring the reproducibility. This function will adjust sequencing depth of a given matrix to a specified total number of reads through random sampling.

Usage

depth.adj(d, size)

Arguments

d	a N*N Hi-C matrix needed to be adjusted.
size	the size the total number one wants to adjust to.

Value

a matrix which has the adjusted total number of reads.

References

HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient. Tao Yang, Feipeng Zhang, Galip Gurkan Yardimci, Fan Song, Ross C Hardison, William Stafford Noble, Feng Yue, Qunhua Li. Genome Research 2017. doi: 10.1101/gr.220640.117

Examples

data(HiCR1)
#total number of reads
sum(HiCR1)

#Adjust it to 200000 reads, output Hi-C matrix
HiC_R1_200k = depth.adj(HiCR1, 200000)
#check total number of reads after adjustment
sum(HiC_R1_200k)

MonkeyLB/hicrep documentation built on Dec. 15, 2020, 12:47 a.m.