HiCKeyR

R package of HiCKey. It has two functions segment(argv) and segHeatMap(argv, s, e).

Install

First, user needs Rcpp and devtools:

install.packages("Rcpp")
install.packages("devtools")
library(devtools)

Then, install the HiCKeyR package:

install_github("https://github.com/YingruWuGit/HiCKeyR.git")
library(HiCKeyR)

segment(argv)

This function is exactly the same as executing the C++ program. It does not return a value, but generates output files containing boundaries (change-points), hierarchical orders and p-values. If the HiC data file has name "xxxx", then the output files are named as "xxxx_output.txt" and "xxxx_TADs.bed" in the same directory.

• argv This parameter is the full path and name of "arguments_HiCKey.txt" containing the arguments setting. Please refer to the HiCKey repository (https://github.com/YingruWuGit/HiCKey) for the arguments setting in "arguments_HiCKey.txt" and the details of output files.

To use it:

Download "BrownianP.txt" from (https://github.com/YingruWuGit/HiCKey/blob/master/BrownianP.txt)

Set the arguments in "arguments_HiCKey.txt", then input:

segment("C:/Users/Andrew/Documents/GitHub/HiCKeyR/arguments_HiCKey.txt")

segHeatMap(argv, s, e)

This function is almost the same as segment(argv). The only difference is that it returns a submatrix of the HiC data, in which the upper triangular part is the original HiC data but the lower triangular part is blockwise constant that constructed from the detected boundaries and their hierarchical orders. User can draw a heatmap by the returned submatrix.

• argv Same as above.
• s Start index of the submatrix. Its default value is 0. Note that the index is 0 based.
• e End index of the submatrix. Its default value is -1, which means the end of the whole HiC matrix. Note that the last index of the submatrix is actually e-1 following C++ convention.
• return It returns a Rcpp::NumericMatrix from s to e. Its upper triangular part is the original HiC data but the lower triangular part is blockwise constant that constructed from the detected boundaries. It also generates two files "xxxx_output.txt" and "xxxx_TADs.bed".

To use it:

Download "BrownianP.txt" from (https://github.com/YingruWuGit/HiCKey/blob/master/BrownianP.txt)

If HiC data is "samp_nested.txt" (https://github.com/YingruWuGit/HiCKey/tree/master/examples), the "arguments_HiCKey.txt" can be

C:/Users/Andrew/Documents/GitHub/HiCKey/examples/samp_nested.txt
C:/Users/Andrew/Documents/GitHub/HiCKey/BrownianP.txt
m
3
0.05
0.00005

Input the following commands in R, leaving s and e as default

X = segHeatMap("C:/Users/Andrew/Documents/GitHub/HiCKeyR/arguments_HiCKey.txt")
heatmap(X, Rowv = NA, Colv = NA, revC = TRUE, scale = "none", col = gray.colors(50, start = 1, end = 0, gamma = 0.15))

The heatmap is

If HiC data is "chr21_50kb.RAWobserved" (https://github.com/YingruWuGit/HiCKey/tree/master/examples) with resolution 50k, then input something like:

X = segHeatMap("C:/Users/Andrew/Documents/GitHub/HiCKey/arguments_HiCKey.txt", 0, 15050000)
heatmap(X, Rowv = NA, Colv = NA, revC = TRUE, scale = "none", col = gray.colors(50, start = 1, end = 0, gamma = 0.15))