Tag: RSQLite

I am a relatively new R-user. I am currently working on trying to read .maf files via the maftools package released by Bioconductor. I am following the instructions as posted on the Bioconductor website (www.bioconductor.org/packages/devel/bioc/vignettes/maftools/inst/doc/maftools.html#4_Installation), however, everytime I attempt to run the installation, it gets stuck on RSQLite and I…

Hello! I am working on analyzing a dataset I created with the 10x Chromium Single Cell Multiome kit. In order to add gene annotation to the ATAC data, I am trying to install and use the “EnsDb.Mmusculus.v79” and “BSgenome.Mmusculus.UCSC.mm10” packages with bioconductor. The same ERROR has come up repeatedly whenever…

Hi, I have a question about DESeq2 LFCshrinkage: Is it possible that some genes have a slightly higher LFC after shrinkage? It happened during my RNAseq DE analysis, I have very deeply sequenced samples with large base means. I tried visualizing using MAplot check, and it looks fine. I’m mainly…

DOI: 10.18129/B9.bioc.lumi     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see lumi. BeadArray Specific Methods for Illumina Methylation and Expression Microarrays Bioconductor version: 3.12 The lumi package provides an integrated solution for the Illumina microarray data analysis. It includes functions of Illumina…

Dear Bioc, Following the rtracklayer documentation, section 2.2.4, ‘A Shortcut’, I encounter the following error browseGenome (subTargetTrack) Error in validObject(.Object) :invalid class “ucscCart” object: superclass “ANYTHING” not defined in the environment of the object’s class traceback () 13: stop(msg, ” “, errors, domain = NA)12: validObject(.Object)11: initialize(value, …)10: initialize(value, …)9:…

I have installed DESeq2 version 1.36.0 samples <- colnames(txi$counts) group <- as.factor(c(“control”,”control”,”control”,”control”,”control”,”diet”,”diet”,”diet”,”diet”,”diet”, “control”,”control”,”control”,”control”,”control”,”diet”,”diet”,”diet”,”diet”,”diet”,”diet”)) coldata <- data.frame(samples, group, stringsAsFactors = F) coldata <- coldata[,c(“samples”,”group”)] coldata$samples <- factor(coldata$samples) coldata$group <- factor(coldata$group) rownames(coldata) <- sub(“fb”, “”, rownames(coldata)) all(rownames(coldata$samples) %in% colnames(txi)) all(rownames(coldata) == colnames(txi)) TRUE library(DESeq2) ddsTxi <- DESeqDataSetFromTximport(txi, colData = coldata, design =…

deseq2 problem 0 Hi I am trying to draw a PCA plot with DESeq2 but somehow I cannot use DESeq2 functions. It is a really simple code i wil be pasting below. > transform <- DESeq2::rlog(eliminated_data, blind = TRUE) Error in (function (classes, fdef, mtable) : unable to find an…

GDCprepare of RNAseq counts produces error 1 @76ac7b25 Last seen 12 minutes ago Canada Hello everyone! I have been using the TCGAbiolinks package for the last couple years to access RNAseq data for the TCGA-LAML project. Just very recently, I had noticed that I could no longer use GDCquery to…

Dear friends, We are trying to use Salmon for DTU analysis. We want to separate exogenous from endogenous transcripts by following this post www.biostars.org/p/443701/ and this paper f1000research.com/articles/7-952 We are focusing on a gene called ASCL1 (endo-ASCL1). We transduced cells with lentiviral vector containing ASCL1 ORF only (Lenti-ASCL1). There should…

GDCquery_Maf error 0 @76e1237b Last seen 1 day ago Singapore Hi all, I really need some help. I am trying to run GDCquery_Maf which worked fine until yesterday. Now I get the following error: Error in GDCquery(paste0(“TCGA-“, tumor), data.category = “Simple Nucleotide Variation”, : Please set a valid workflow.type argument…

subpopulations available in MafH5.gnomAD.v3.1.1.GRCh38 1 @b14a6f0d Last seen 16 hours ago United States Are subpopulation MAFs available for gnomADv.3.1.1 with any package, like they are in MafDb.gnomAD.r2.1.hs37d5? I’m trying to use Genomic Scores to obtain all variants in a genomic range with MAF in any subpopulation >= cutoff. I tried…

Why do you specify y = I(list(7,6)) instead of y=c(6,7)? This seems to work: dbGetQuery (c, “select * from tst where x = ? and y in (?)”, data.frame(x=1, y=c(7,6))) You might be looking for expand.grid. dbGetQuery (c, “select * from tst where x = ? and y in (?)”,…

Python Javascript Linux FAQ LoginSignup PUBLIC All Questions Tags Snippets Jobs rsqlitersqlite rsqlitedata-tablesqliter rsqlitersqlite sqlrdatabasersqlite sqlrprepared-statementrsqlitedatabase rr-markdowndata-wranglingrsqlitesql rrsqlitesqlite rsqliter-dbir rsqlitersqlite sqldfrrsqlite PreviousNext Recent Posts show same id one time but in column count how many times php Assign bundle or argument to ImageView in Android ValueRequiredException during RSS feed parsing…

Dear Friends, I have been having considerable difficulty doing various package related bioconductor actions. Here is my system specifications: ======================================================================= macOS Monterey Version: 12.3 (21E230) MacBook Pro (Retina, 13-inch, Early 2015) Memory: 16 GB 1867 MHz DDR3 RStudio 2021.09.0 Build 351 R version 4.1.2 (2021-11-01) — “Bird Hippie” Copyright (C)…

When I try to install the gtf for hg38 BiocManager::install(“TxDb.Hsapiens.UCSC.hg38.knownGene”) I get the following error: ‘getOption(“repos”)’ replaces Bioconductor standard repositories, see ‘?repositories’ for details replacement repositories: CRAN: cran.rstudio.com/ Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.2 (2021-11-01) Installing package(s) ‘TxDb.Hsapiens.UCSC.hg38.knownGene’ Error in readRDS(dest) : error reading from connection Per stackoverflow.com/questions/67455984/getoptionrepos-replaces-bioconductor-standard-repositories-see-reposito I…

python – OperationalError: database is locked I have made some repetitive operations in my application(testing it), and suddenly I’m getting a weird error: OperationalError: database is locked I’ve restarted the server, but the error persists.… how to close resultset in RMySQL? I…

Hello, I have finished the RNA seq analysis and I am trying to perform some pathway analysis. I have used the gage package and I was looking online about another package called goseq that takes into account length bias. However, when I run the code I get an error. How…

Installation of current released version from CRAN install.packages(“rocker”) Installation of current development version from GitHub install.packages(“devtools”) devtools::install_github(“nikolaus77/rocker”) Create new rocker database handling object Option 1 db <- rocker::newDB() # New database handling object #> dctr | New object Option 2 db <- rocker::rocker$new() # New database handling object #> dctr…

DESeq2 and high prefiltering cutoff 1 @255004b1 Last seen 3 hours ago United States Hi, I am curious about prefiltering with DESeq2. I understand from this site and reading the DESeq2 vignette that prefiletering is really unnecessary as DESeq2 has a stringent filtering that it does. However, I’m seeing better…

I now think that the default mode should be to return an error here. That ship has sailed now. SQLite is fairly unique in its flexibility to store arbitrary data in the columns. For your use case I’d recommend segmenting by data type: library(RSQLite) con <- dbConnect(SQLite(), “:memory:”) dbGetQuery(con, “SELECT…

A simple SQLite clone in Rust. This is basically a translation of the C code present on this brilliant tutorial into Rust(not fully idiomatic). This code contains implementation only upto Part 5 in the tutorial. This a very simple database and is a small project I took up to gain…

Hi, I cannot install traviz package (version 1.0.0) from Bioconductor on a linux machine (from source). I have a conda environment, and I installed traviz from conda, but it cannot be used – when I do library(traviz) R just crashes and quits without any message. So I tried to install…

SQLite is a file level database, hence to reference it requires a full directory path. No where do you specify the working directory or a full path in the file name. By default, R will use the current working directory contained in getwd(). If database is not contained in this…

Hi, I’m trying to learn how to use RSQLite but I’m already having a problem, wondered if anyone knows how to fix it. I have a pre-existing database (.data) file which does not have attribute names and I am trying to create a SQLite database with a table defined with…

Description Copies a database connection to a file or to another database connection. It can be used to save an in-memory database (created using dbname = “:memory:” or dbname = “file::memory:”) to a file or to create an in-memory database a copy of another database. Usage sqliteCopyDatabase(from, to) Arguments from…

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Wed, 29 Dec 2021 01:12:39 +0530 Source: r-cran-rsqlite Architecture: source Version: 2.2.9-1 Distribution: unstable Urgency: medium Maintainer: Debian R Packages Maintainers <r-pkg-t…@alioth-lists.debian.net> Changed-By: Nilesh Patra <nil…@debian.org> Changes: r-cran-rsqlite (2.2.9-1) unstable; urgency=medium . * Team Upload. [ Andreas Tille ] * Disable…

You’re not using the pattern suggested by the RSQLite documentation. That documentation uses dbWriteTable to copy a data frame into a SQLite table: dbWriteTable(con, “mtcars”, mtcars) According to this documentation, your full code would look something like this: con <- dbConnect(RSQLite::SQLite(), “./mtcars.db”) data(mtcars) dbWriteTable(con, “mtcars”, mtcars) dbListTables(con) # Fetch all…

UPDATE: newest versions of RSQLite and sqldf do not have the incompatibility issues addressed by this question i.e.: sqldf_0.4-10 RSQLite_1.1-2 work together well – Nathan All: Thanks to G. Grothendieck for pointers to incompatibility issues introduced by RSQLite 1.1-1. As stated in the comment to the answer, downgrade RSQLite to…

GenomicFeatures::makeTxDbFromUCSC failing with an error: identical(current_classes, .UCSC_TXCOL2CLASS) is not TRUE 1 @mikhail-dozmorov-23744 Last seen 1 day ago United States Hi,The GenomicFeatures::makeTxDbFromUCSC function fails with: library(GenomicFeatures) > hg19.refseq.db <- makeTxDbFromUCSC(genome=”hg19″, table=”refGene”) Download the refGene table … Error in .fetch_UCSC_txtable(genome(session), tablename, transcript_ids = transcript_ids) : identical(current_classes, .UCSC_TXCOL2CLASS) is not TRUE OK The…

I am trying to scrape some pitchf/x data and store it in an SQLite database. However, I am receiving the following error when I run the following code: library(RSQLite) library(dplyr) db <- src_sqlite(“pitchfx.sqlite3”, create = T) This is the error: Error in h(simpleError(msg, call)) : error in evaluating the argument…

Hello, I am using DESeq2 for analysis of RNAseq data. I would like to ask you about the design in the DESEq2 formula. I have tissue from animals treated with a chemical and my animal model is a colorectal cancer model. My variables are gender (male or female), treatment (treated…

I’m using RSQlite to import Datasets from an SQlite-Database. There are multiple millions of observations within the Database. Therefor I’d like to do as much as possible of Data selection and aggregation within the Database. At some point I need to aggregate a character variable. I want to get the…

    This package is for version 2.14 of Bioconductor; for the stable, up-to-date release version, see pd.ht.hg.u133a. Platform Design Info for The Manufacturer’s Name HT_HG-U133A Bioconductor version: 2.14 Platform Design Info for The Manufacturer’s Name HT_HG-U133A Author: Benilton Carvalho Maintainer: Benilton Carvalho <beniltoncarvalho at gmail.com> Citation (from within R,…

    This package is for version 2.14 of Bioconductor; for the stable, up-to-date release version, see pd.hg.focus. Platform Design Info for The Manufacturer’s Name HG-Focus Bioconductor version: 2.14 Platform Design Info for The Manufacturer’s Name HG-Focus Author: Benilton Carvalho Maintainer: Benilton Carvalho <beniltoncarvalho at gmail.com> Citation (from within R,…

    This package is for version 2.14 of Bioconductor; for the stable, up-to-date release version, see pd.raex.1.0.st.v1. Platform Design Info for Affymetrix RaEx-1_0-st-v1 Bioconductor version: 2.14 Platform Design Info for Affymetrix RaEx-1_0-st-v1 Author: Benilton Carvalho Maintainer: Benilton Carvalho <Benilton.Carvalho at cancer.org.uk> Citation (from within R, enter citation(“pd.raex.1.0.st.v1”)): Installation To…

I have an RNAseq dataset, where one of the genes I intend to analyze has hundreds of counts ranging from 10 to 12, with a few counts > 9000. I process this data in Deseq2 and get that the gene is differentially expressed across several samples of interest. What can…

    This package is for version 2.8 of Bioconductor; for the stable, up-to-date release version, see pd.feinberg.mm8.me.hx1. Platform Design Info for NimbleGen feinberg_mm8_me_hx1 Bioconductor version: 2.8 Platform Design Info for NimbleGen feinberg_mm8_me_hx1 Author: Martin Aryee Maintainer: Martin Aryee <aryee at jhu.edu> Citation (from within R, enter citation(“pd.feinberg.mm8.me.hx1”)): Installation To…

Hi, every one. I find a werid MAplot or volcano plot of DESeq reuslt. I am wondering whether you can give me some advice. This diff result is from two cell type bulk RNA-seq. I use two specific marker to get these two cell type using Flow cytometer. I alreadly…