User: remi.tournebize

Reputation:
10
Status:
New User
Location:
France
Last seen:
2 years, 9 months ago
Joined:
2 years, 12 months ago
Email:
r**************@gmail.com

Posts by remi.tournebize

<prev • 10 results • page 1 of 1 • next >
0
votes
2
answers
542
views
2
answers
Answer: A: Automatic NA values generated by the ld() function of snpStats package
... Dear Vincent, Many thanks for your insight. Now it gets clear for me. Best regards, Rémi ...
written 2.8 years ago by remi.tournebize10
0
votes
2
answers
2.1k
views
2
answers
Answer: A: new package `ggtree` in devel branch
... Hello, This is a neat package! Is it possible by any mean to plot onto tree branches points at given times (not simply at the nodes)? Thank you for this great job, hope the package will be stable released soon, Rémi ...
written 2.8 years ago by remi.tournebize10
1
vote
2
answers
542
views
2
answers
Automatic NA values generated by the ld() function of snpStats package
... Dear list, When using the ld() function (to compute linkage disequilibrium indices) from snpStats package of BioConductor, one can get automatic NA values in many rows or columns of the LD matrix (whatever the statistic being used, e.g. R², D', etc.). This phenomenon happens even if there is no NA ...
0
votes
5
answers
585
views
5
answers
Answer: A: Filter every X position
... Many thanks Martin and Hervé! Wishing you a very happy new year, Rémi ...
written 2.9 years ago by remi.tournebize10
0
votes
5
answers
585
views
5
answers
Comment: C: Filter every X position
... Dear Julian and Hervé, "Relevant" might be an unappropriate adjective. My objective is to filter a dataset of SNPs for demographic studies. One priority for my models is to consider SNPs assumed to be independent. To do so, I have calculated a mean LD distance and want to extract SNPs which are loc ...
written 2.9 years ago by remi.tournebize10
0
votes
5
answers
585
views
5
answers
Answer: A: Filter every X position
... Dear Julian and Martin, thank you so much for your messages and propositions. Julian, I wrote this script initially but the problem of the diff function is that it computes the difference between consecutive pairs of array elements. Thus, if I have for instance an array 0 50 60 70 100 And a thres ...
written 2.9 years ago by remi.tournebize10
4
votes
5
answers
585
views
5
answers
Filter every X position
... Dear all, I would like to filter the SNPs of a VCF file so to extract only SNPs distant of X kb between each other. I do not see any built-in function to perform this kind of filtering so aimed at writing a filter rule to achieve it and pass it through the filterVcf function of the VariantAnnotatio ...
variantannotation written 2.9 years ago by remi.tournebize10
0
votes
0
answers
110
views
0
answers
Comment: C: Filtering SNP every X positions
... Edit. I think the function to extract position information could be ranges() from the IRanges library. ...
written 3.0 years ago by remi.tournebize10
0
votes
2
answers
1.2k
views
2
answers
Answer: A: VariantAnnotation Installation Error RSQLite
... Dear James, Yes, the RSQLite package works well for the old version 0.11.4. It seems the youngest version of R (3.2.1) can fix the problem... at least on Windows. Best regards, Rémi ...
written 3.0 years ago by remi.tournebize10
0
votes
2
answers
1.2k
views
2
answers
VariantAnnotation Installation Error RSQLite
... Hello everyone, I am having problems installing the VariantAnnotation library of Bioconductor in R version 3.0.1. I have tried installing the library using RSQLite new version 1.0.0 and old version 0.11.4 but I still got a message error (its content depending on the version of the installed RSQLit ...
variantannotation rsqlite written 3.0 years ago by remi.tournebize10

Latest awards to remi.tournebize

Popular Question 2.7 years ago, created a question with more than 1,000 views. For VariantAnnotation Installation Error RSQLite

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 392 users visited in the last hour