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User: Vinicius Henrique da Silva

Reputation:
20
Status:
New User
Location:
Brazil
Last seen:
1 month ago
Joined:
4 years, 5 months ago
Email:
v*****************@hotmail.com

Posts by Vinicius Henrique da Silva

<prev • 41 results • page 1 of 5 • next >
2
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1
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70
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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 4 weeks ago by Vinicius Henrique da Silva20 • updated 4 weeks ago by Marcel Ramos ♦♦ 350
2
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1
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141
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1
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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 7 months ago by Vinicius Henrique da Silva20 • updated 7 months ago by Aaron Lun22k
0
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1
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195
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1
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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 9 months ago by Vinicius Henrique da Silva20 • updated 9 months ago by zhengx20
0
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1
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245
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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 13 months ago by Vinicius Henrique da Silva20
1
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1
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245
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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 13 months ago by Vinicius Henrique da Silva20 • updated 13 months ago by Erik Wright130
0
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0
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377
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0
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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 2.1 years ago by Vinicius Henrique da Silva20
2
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1
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398
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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 2.1 years ago by Vinicius Henrique da Silva20 • updated 2.1 years ago by bernatgel90
0
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1
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482
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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 2.5 years ago by Vinicius Henrique da Silva20 • updated 2.4 years ago by Hervé Pagès ♦♦ 13k
0
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315
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Fill the color in a graph in a reverse scale - gtrellis
...    I would like to fill the graph within the polygons instead out of it.  library(gtrellis) library(circlize) tiff("plot.tiff", units="in", width=11, height=8.5, res=300, compress = "lzw") load(system.file("extdata", "DMR.RData", package = "circlize")) DMR_hyper_density = ci ...
gtrellis written 2.6 years ago by Vinicius Henrique da Silva20
0
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306
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Plot just one y label in gtrellis
... I would like to plot just one y-axis label for each different track instead one for each chromosome in gtrellis package (In the manual example exemplified below the title "density" is repeated several times). I tried to modify the track_ylab parameter but it don't allows to specify which tracks must ...
gtrellis written 2.6 years ago by Vinicius Henrique da Silva20

Latest awards to Vinicius Henrique da Silva

Popular Question 5 weeks 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 9 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 2.8 years ago, voted at least 25 times.

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