Comments (2)
Hi - I will remove that hard limit in the code.
For this code (matrix2insulation) the memory usage will scale with your selected insulation square size * nrow/ncol.
So memory usage should always be low [MBs] given normal usage.
We only load into memory N diagonals up to your specified insulation square size.
e.g.
1,000,000bp square size for a 5KB binned matrix would load into memory ~400 diagonals.
This script is more intended for matrices < 10,000 x 10,000.
For the higher resolution data and larger matrices, a more efficient data format (sparse, hdf5, etc) would be more ideal, though this script may still work.
I tested the code on a ~50,000 x ~50,000 matrix, it takes quite a bit of time (15 minutes) to run. Mainly to simply read the gzipped txt file, but it does complete AOK.
Script will work for any species, as long as the matrix is binned into equal sized intervals, and the intervals are formatted in the my5C format.
https://github.com/blajoie/crane-nature-2015/wiki
e.g. bin1|hg19|chr1:40000-80000
The code is updated now, give it another shot!
from crane-nature-2015.
issue looks to be fixed now! closing this.
from crane-nature-2015.
Related Issues (12)
- Input matrix header / rownames HOT 2
- how to calculate the insulation score for higher resolution Hi-C data HOT 1
- The boundary strength was defined as the difference in the delta vector
- no
- how to use insulation score to identify TAD domains HOT 3
- Some boundaries are local maximum of insulation score profile instead of local minimum HOT 2
- overlap between different boundaries HOT 1
- different insulation scores between *.insulation file and *.insulation.boundaries file HOT 2
- how to create the input matrix? HOT 2
- an error in the usage
- how get TADs with a matrix from HiCPro? HOT 11
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from crane-nature-2015.