Comments (2)
Hi David,
you can omit the minor allele from the column names by creating the BEDMatrix object using X <- BEDMatrix(file, simple_names = TRUE)
. The output values are allelic dosages (0/1/2/NA), counting the number of minor alleles.
Hope that helps,
Alex
from bedmatrix.
Hi David,
you can omit the minor allele from the column names by creating the BEDMatrix object using
X <- BEDMatrix(file, simple_names = TRUE)
. The output values are allelic dosages (0/1/2/NA), counting the number of minor alleles.Hope that helps, Alex
Thank you for your prompt response. I think that the number is just the coding for a category regarding if it is minor allele homozygus (0: in case the variation in C>T... it would be TT; thats why is minor) and then heterozygus (eg, 1: CT) and major allele homozygus (2 : eg, CC)
i found this:
https://www.cs.cmu.edu/~sssykim/teaching/s13/slides/Lecture1.pdf
So, it would actually count the number of Major alleles (I mean, seems to be that way)
from bedmatrix.
Related Issues (20)
- Check for user interrupts HOT 1
- Support individual-major mode HOT 1
- Speed up determination of number of lines HOT 2
- Extract ranges more efficiently HOT 1
- Add range checks HOT 1
- Adapt tests to new dataset
- BEDMatrix error HOT 2
- Add parameter to set madvise HOT 1
- installation error for R version 3.4.1 HOT 2
- error message on convertIndex HOT 10
- Mutualize code HOT 5
- Error in BEDMatrix(bd1) : File not found. HOT 1
- BEDMatrix instance has been unmapped HOT 1
- Support replacement HOT 2
- Experiment with S3 conversion
- Test on Windows and Mac HOT 1
- Support single indexes HOT 4
- Eliminate compiler warnings HOT 1
- automatically detect number of markers in .bim file HOT 4
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 bedmatrix.