User: Vinicius Henrique da Silva

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

Posts by Vinicius Henrique da Silva

<prev • 40 results • page 1 of 4 • next >
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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 11 weeks ago by Vinicius Henrique da Silva20 • updated 11 weeks ago by Aaron Lun21k
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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 4 months ago by Vinicius Henrique da Silva20 • updated 4 months ago by zhengx20
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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 8 months ago by Vinicius Henrique da Silva20
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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 8 months ago by Vinicius Henrique da Silva20 • updated 8 months ago by Erik Wright130
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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 20 months ago by Vinicius Henrique da Silva20
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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 20 months ago by Vinicius Henrique da Silva20 • updated 20 months ago by bernatgel90
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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 2.1 years ago by Vinicius Henrique da Silva20 • updated 2.0 years ago by Hervé Pagès ♦♦ 13k
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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 2.2 years ago by Vinicius Henrique da Silva20
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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 2.2 years ago by Vinicius Henrique da Silva20
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Comment: C: DECIPHER version bug using biocLite()
... Hi Julian. Please check my update. I was unable to identify what was wrong with my versions.  ...
written 2.3 years ago by Vinicius Henrique da Silva20

Latest awards to Vinicius Henrique da Silva

Popular Question 4 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 2.4 years ago, voted at least 25 times.

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