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This package was developed in R version 3.6.2, back compatability is not guaranteed
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To use this package, you need a compiler that has support for C++11, such as
- GCC: see here, for example
- clang: see here
Installation is easy with the R package devtools. If you don't already have devtools installed, you will first need to type (from within R)
install.packages("devtools")With devtools installed, simply enter the following:
devtools::install_github("hillarykoch/locdiffr", build_vignettes = TRUE)Installation may take a couple of minutes due to building the vignette. The vignette contains all of the necessary instructions to run locdiffr. To view the vignette, enter the following within R:
browseVignettes(package = "locdiffr")To begin the analysis, you need file paths to all of the data, split into two groups. The data should be in the following tab-delimited format:
| Loc1 | Loc2 | Counts |
|---|---|---|
| 0 | 0 | 100 |
| 0 | 50000 | 88 |
| 0 | 100000 | 40 |
Here, Loc1 is the start of the first bin, Loc2 the start of the second bin, and counts indicating the read counts for the interactions between those 2 bins. The value in Loc1 should always be less than or equal to the value in Loc2. An individual dataset is intended to be Hi-C data from an entire chromosome. Chromosomes should be analyzed separately.