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DESCRIPTION
NAMESPACE
README.md
limacc.Rproj
limacc4command
limacc_withArgs.R

README.md

LiMACC

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

library(devtools)
install_github("wbaopaul/limacc")

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)

Note

  • The latest limacc needs R version 3.5.1 or later

Required Inputs

  • 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'

Output

  • A data frame providing the significant interactions
  • The significant interactions were also saved in a file with user specificed file name

Help in R

library(limacc)
help(limacc)

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

    ./limacc4command --help
    

Reference

The detailed information of LiMACC algorithm is described in the following paper:

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