User: Vinicius Henrique da Silva

Reputation:
30
Status:
New User
Location:
Brazil
Last seen:
1 month ago
Joined:
4 years, 8 months ago
Email:
v*****************@hotmail.com

Posts by Vinicius Henrique da Silva

<prev • 43 results • page 1 of 5 • next >
2
votes
1
answer
113
views
1
answer
Make UpSet function display numbers above the bars
... I am using the `ComplexHeatmap` package to represent the intersection among different `GRanges`. The vignette has some nice example to plot it: library(circlize) library(ComplexHeatmap) library(GenomicRanges) lt2 = lapply(1:4, function(i) generateRandomBed()) lt2 = lapply(lt2, f ...
complexheatmap written 7 weeks ago by Vinicius Henrique da Silva30 • updated 7 weeks ago by Zuguang Gu40
2
votes
1
answer
128
views
1
answer
Create a matrix to show overlaps among multiple GRanges
... I am trying to find a way to efficiently extract a matrix showing '0' or '1' when comparing different `GRange` objects. In my example: gr.1 <- regioneR::createRandomRegions(nregions=1000, length.mean=500000, length.sd=30000) gr.2 <- regioneR::createRandomRegions(nregions=1000, length. ...
genomicranges granges R written 7 weeks ago by Vinicius Henrique da Silva30 • updated 7 weeks ago by James W. MacDonald49k
2
votes
1
answer
116
views
1
answer
Go back to GRanges used as RaggedExperiment input
... I am trying to get back to the input objects of a RaggedExperiment object. Using the example in the manual: sample1 <- GRanges( c(A = "chr1:1-10:-", B = "chr1:8-14:+", C = "chr2:15-18:+"), score = 3:5) sample2 <- GRanges( c(D = "chr1:1-10:-", E = "chr2:11-18:+" ...
raggedexperiment written 3 months ago by Vinicius Henrique da Silva30 • updated 3 months ago by Marcel Ramos ♦♦ 360
2
votes
1
answer
177
views
1
answer
Error to rename seqlevels in Granges interactions
... I am trying to rename the seqlevels in an interactionSet object. The syntax for common GRanges don't work in an interaction set. Any ideas how to make it work then?   library(GenomicRanges) gr <- GRanges(rep(c("chr2", "chr3", "chrM"), 2), IRanges(1:6, 10)) index.epistasis <- expand.grid( ...
granges interactionset written 9 months ago by Vinicius Henrique da Silva30 • updated 9 months ago by Aaron Lun23k
0
votes
1
answer
231
views
1
answer
Write gds in parallel
... I am trying to write values at a certain GDS node in parallel. I was not able to figure out what I am doing wrong. I have tried the following: ​# Load data data(hapmap_geno) # Create a gds file snpgdsCreateGeno("test.gds", genmat = hapmap_geno$genotype, sample.id = hapmap_geno$sample.id, snp ...
biocparallel snprelate gds written 11 months ago by Vinicius Henrique da Silva30 • updated 11 months ago by zhengx20
0
votes
1
answer
271
views
1
answers
Comment: C: Transform index to chromosome in DECIPHER package
... Hi Erik, thank you for your prompt answer. In your example you used 'XStringSet; instead 'FASTA' directly. Running the analysis again using your example will work fine. However, would be nice to understand what I have already, where I used the 'FASTA' files. As far I understand, the 'Seqs2DB' functi ...
written 15 months ago by Vinicius Henrique da Silva30
1
vote
1
answer
271
views
1
answer
Transform index to chromosome in DECIPHER package
... I am trying to understand how the index from the synteny analysis in the DECIPHER package can be translated into chromosomes. I basically used what is in the official website: # load the DECIPHER library in R library(DECIPHER) # specify the path to each FASTA file (in quotes) # each genome must b ...
decipher written 15 months ago by Vinicius Henrique da Silva30 • updated 15 months ago by Erik Wright130
0
votes
0
answers
415
views
0
answers
Avoid 'dStr8' format in the GDS files
... I would like to use a GDS file to an external software called SNPhylo. However, I am getting an error when trying to use this external software:   Error in index.gdsn(gdsobj, "sample.id") : No class name 'dStr8' in the GDS system. Reading the news about the GDS files in GitHub, this 'dStr8' forma ...
snprelatesnp written 2.3 years ago by Vinicius Henrique da Silva30
2
votes
1
answer
440
views
1
answer
Conflicting results in 'overlapPermTest' function from regioneR package
... I am aware that non-reproducible questions are annoying. However, I am not sure how to reproduce my problem without my original data (and consequently to large to be included here).  I have two groups of genomic ranges, 'Nre' and 'Re', and I compared separately how random are their overlap with CpG ...
regioner written 2.3 years ago by Vinicius Henrique da Silva30 • updated 2.3 years ago by bernatgel90
0
votes
1
answer
511
views
1
answer
Identify in tandem repeats with Bioconductor
... I would like to identify the regions with repeated patterns in a given genome. Let's say that I need to identify [TA]n regions, were 'n' is a variable number of repeats. I thought in a loop to resolve the problem, however, it will take a long time and will produce redundant regions. Thus, I would l ...
biostrings written 2.6 years ago by Vinicius Henrique da Silva30 • updated 2.6 years ago by Hervé Pagès ♦♦ 13k

Latest awards to Vinicius Henrique da Silva

Popular Question 3 months ago, created a question with more than 1,000 views. For Error: package ‘snpMatrix’ is not available (for R version 3.2.2)
Popular Question 11 months ago, created a question with more than 1,000 views. For Error: package ‘snpMatrix’ is not available (for R version 3.2.2)
Supporter 3.0 years ago, voted at least 25 times.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 269 users visited in the last hour