depth.adj {hicrep} | R Documentation |
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.
depth.adj(d, size, resol, out = 0)
d |
a Hi-C matrix needed to be adjusted. |
size |
the size the total number one wants to adjust to. |
resol |
the resolution of the input matrix. |
out |
either 0 or 1. If it is 0, the function returns matrix format; if 1, it returns vection format. |
a matrix or vec which has the adjusted total number of reads.
HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient. Tao Yang, Feipeng Zhang, Galip Gurkan Yardimci, Ross C Hardison, William Stafford Noble, Feng Yue, Qunhua Li. bioRxiv 101386; doi: https://doi.org/10.1101/101386.
data(HiCR1) #total number of reads sum(HiCR1[,-c(1:3)]) #Adjust it to 200000 reads, output Hi-C matrix HiC_R1_200k = depth.adj(HiCR1, 200000, 1000000, out = 0) #check total number of reads after adjustment sum(HiC_R1_200k[,-c(1:3)]) #output vector HiC_R1_200k = depth.adj(HiCR1, 200000, 1000000, out = 1) #check total number of reads after adjustment sum(HiC_R1_200k[,3])