User: Welliton Souza

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70
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Trusted
Location:
Brazil
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https://welliton309.gi...
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welliton309
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2 months ago
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3 years, 2 months ago
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Posts by Welliton Souza

<prev • 12 results • page 1 of 2 • next >
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Comment: C: Printing DataFrame with nested DataFrames causes error
... Thank you Hervé for the explanation. It was very clarifying. I think the fix in development version worked for me. I agree with you and Michael about behavior of DataFrame being the consistent with base data.frame.  ...
written 9 months ago by Welliton Souza70
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Comment: C: Printing DataFrame with nested DataFrames causes error
... Thank you Michael. I updated my R installation and I got the latest version of the S4Vectors package. The error does not occur anymore. I expected the DataFrame object itself instead of a list. I tested the Hervé's example with base data frames and the behavior was the same. ...
written 9 months ago by Welliton Souza70
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Comment: C: Printing DataFrame with nested DataFrames causes error
... Thank you Martin for the comment. Actually, the nested data frames may have different shapes (number of columns and rows). This data I am working on came from web APIs (using httr and jsonlite packages). I will update my example. ...
written 9 months ago by Welliton Souza70
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Printing DataFrame with nested DataFrames causes error
... I would like to use DataFrame class to represent data.frame with nested data frames. For example, a data frame that have a list of data frame as column (one data frame for each row). library(S4Vectors) df <- DataFrame(a=c(1,2,3), b=c("a","b","c")) df Outputs: DataFrame with 3 rows and 2 colu ...
s4vectors dataframe written 9 months ago by Welliton Souza70 • updated 9 months ago by Hervé Pagès ♦♦ 13k
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Answer: A: Rqc - envir must be either NULL, a list, or an environment.
... Hi guus.steeg, thank you for posting this issue. I am the developer of Rqc package. The rqc and rqcQA functions should return a list of RqcResultSet objects. When you pass only one input file these functions return the object itself, which make the other functions fail (my fault). A workaround for ...
written 9 months ago by Welliton Souza70
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Answer: A: Rqc aborts with error corrupted double-linked list with valid fastq
... Hi paucarrio, Thank you for sharing this issue. I reproduced your error and I found a bug in internal function of Rqc package. I will fix this error soon as possible. The code below is a workaround for this issue. library(Rqc) # replace internal function code to avoid the bug .readFrequency < ...
written 10 months ago by Welliton Souza70
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Does bsseq package work with technical replicates?
... I would like to know whether bsseq package works with technical replicates (i.e. two whole-genome bisulfite sequencing of the same DNA sample). How bsseq deal with replicate information? The code below exemplifies what I have done. > pData(bismarkBSseq) DataFrame with 8 rows and 2 columns ...
bsseq wgbs written 11 months ago by Welliton Souza70
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Answer: A: packages installation problem
... When you facing with a dependency error problem, you can try to install the package that other packages depend on it. In your case, I guess is the annotate package. Then try to install only this package. An example: library(BiocInstaller) biocLite("annotate") And see what is the error related to ...
written 21 months ago by Welliton Souza70
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Answer: A: Rqc for RNA-Seq data
... Rqc automatically process multiple files in parallel. The multicoreWorkers function returns the number of available processing units. The rqc function generates only one report file for all FASTQ files. The output directory of report file is defined by outdir parameter and the name of the report fi ...
written 21 months ago by Welliton Souza70
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Answer: A: Rqc for RNA-Seq data
... The rqc function uses list.files function to search a pattern inside a folder defined by the path. You can run list.files first with the same parameters to see which files the rqc funtion will process. An exemple (using your path): folder <- "/home/Downloads/Work_Kriti/NGS_Data" list.files(path ...
written 21 months ago by Welliton Souza70

Latest awards to Welliton Souza

Scholar 9 months ago, created an answer that has been accepted. For A: Rqc - envir must be either NULL, a list, or an environment.

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