LiMACC is an framework of calling significant interactions from multiple types of chromosome conformation capture assays, including Capture-C, Capture-HiC and HiChIP experiments. It's implemented through a R package limacc.
Install from Github
Install from source codes
- Download source codes here and In R type:
install.packages('path to limacc_1.0.tar.gz', type = 'source', rep = NULL)
- The latest limacc needs R version 3.5.1 or later
fragment_file A bed file (or in similar format) indicates the genomic coordinates of either the restriction enzyme fragments for Capture-C, Capture-HiC, or the binned fragments, in 5kb for instance, for HiChIP data.
- for Capture-C or Capture-HiC data, an example of fragment_file (chromosome start end fragment_id) to indicate the genomic location of the HindIII enzyme fragment :
chr1 0 3002504 chr1_1 chr1 3002504 3005876 chr1_2 chr1 3005876 3006265 chr1_3 ......
- An example of fragment_file (chromosome start end fragment_id) in 5kb resolution for HiChIP is given similarly:
chr1 0 5000 1 chr1 5000 10000 2 chr1 15000 20000 3 ......
Note that the fourth column fragment_id could be any user specified character
contact_file contact matrix file, a three column file with columns (bin_i bin_j count):
chr1_10 chr1_11 2 chr1_10 chr1_15 4 chr1_15 chr1_20 5 ......
Note that the first two columns in the contact_file should be included in the fourth column of the fragment_file.
dtype data type, 'CHiC', 'CC' or 'HiChIP'
peakFile4HiChIP Bed file of 1D peak as virtual viewpoints for HiChIP, set as NULL for dtype is not 'HiChIP'
- A data frame providing the significant interactions
- The significant interactions were also saved in a file with user specificed file name
Help in R
Alternative run through bash command line (for Linux and maxOS)
copy scripts limacc4command and limacc_withArgs.R in this reporitory to the same directory, for example, current directory, then
./limacc4command -f your_fragment_file -c your_contact_file1,file2 -t CHiC
for more help, see
The detailed information of LiMACC algorithm is described in the following paper: