vstran: Variance stablization transformation
In qunhualilab/hicrep: Measuring the reproducibility of Hi-C data

Description Usage Arguments Details Value Examples

The function finds the rank of the data and rescale the ranks in the range of (0, 1).

vstran(d)

`d`	a matrix or data.frame that has two columns, each column is the Hi-C read counts data in a replicate.

In Hi-C data, the read counts for contacts with short interaction distances have a much larger dynamic range than those with long interaction distances. To mitigate this difference, we rank the contact counts in each stratum separately, and then normalize the ranks by the total number of observations in each stratum, such that all strata share a similar dynamic range.

a matrix of two columns, each represents a transformed read counts of a replicate.

data(HiCR1)
data(HiCR2)

#exact contact counts within 1Mb interaction distance
d1 <- d2 <- NULL
for (i in 1:nrow(HiCR1)){
    d1 = c(d1, HiCR1[i, i+1])
    d2 = c(d2, HiCR2[i, i+1])
    d = cbind(d1, d2)
}

HiC_R1_vs <- vstran(d)
head(HiC_R1_vs)