pairCoo2cmap - paired COO sparse matrix to ccmap or gcmapΒΆ
This format is very similar to COO format with an additional information of chromosome. Therefore, maps for all chromosome could be contained in a single file.
This type of format appeared with this publication (GEO datasets).
Following file format can be read as a text file, where first and second column is location on chromosome and third column is the value:
chr4 60000 75000 chr4 60000 75000 0.1163470887070292
chr4 60000 75000 chr4 105000 120000 0.01292745430078102
chr4 60000 75000 chr4 435000 450000 0.01292745430078102
chr4 75000 90000 chr4 75000 90000 0.05170981720312409
chr4 75000 90000 chr4 345000 360000 0.01292745430078102
chr4 90000 105000 chr4 90000 105000 0.01292745430078102
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- Usage:
usage: gcMapExplorer pairCoo2cmap [-h] [-i maps.txt] [-ccm RawObserved] [-od OUTDIR] [-gcm inOut.gcmap] [-cmeth lzf] [-dmeth sum] [-wd /home/rajendra/deskForWork/scratch]
Optional arguments:
-h, --help show this help message and exit
-i maps.txt, --input maps.txt
Input file name.
-ccm RawObserved, --ccmap RawObserved
Use this to convert all contact maps to ccmaps file. Provide suffix of
ccmap file names with this option and it will enable the conversion.
Output ccmap file name is generated automatically as follows;
<chromosome>_<resolution>_<suffix>.ccmap
Note that -od/--out-dir option is also required because all ccmaps will be
saved in this directory.
-od OUTDIR, --out-dir OUTDIR
Directory where all ccmap files will be saved.
-gcm inOut.gcmap, --gcmap inOut.gcmap
Provide gcmap file to convert all contact maps into one gcmap file.
File name should contain full path because -od/--out-dir is not considered
for thi conversion.
-cmeth lzf, --compression-method lzf
Data compression method for gcmap file.
-dmeth sum, --downsample-method sum
Downsampling method to coarsen the resolution in gcmap file. The option is
intended to use with -gcm/--gcmap option. Three accepted methods are
sum : sum of values,
mean : Average of values and
max : Maximum of values.
This option generates all coarser maps where resolutions will be coarsened by
a factor of two, consecutively. e.g.: In case of 10 kb input resolution,
downsampled maps of "20kb", "40kb", "80kb", "160kb", "320kb" etc. will be
generated until, map size is less than 500.
-wd /home/rajendra/deskForWork/scratch, --work-dir /home/rajendra/deskForWork/scratch
Directory where temporary files will be stored.