Bioconductor Forum

of chromosome column. Except for the common 22 pairs of chromosome and X, Y, some other chromosome names are strange to me like CHR\_HSCHR17\_2\_CTG5, MT, CHR\_HSCHR8\_3\_CTG1, CHR\_HSCHR7\_3\_CTG4\_4... Could you please

homo sapiens chromosome

updated 7.6 years ago • xchen8

PM, Jiang, Mike <wjiang2@scharp.org> wrote:<br/> > <br/> > sorry, It is the 'name' column of pData that should be updated. e.g.<br/> > pData(fs)[["name"]] <- c("s1", "s2")<br/> > <br/> > Mike<br/> > ________________________________________...gt; <…

flowviz flowcore

updated 10.4 years ago • Jiang, Mike

<div class="preformatted">On Mon, May 31, 2010 at 9:41 AM, Mervi Kinnunen <mervi.kinnunen@wri.fi>wrote: > Hi, > > > > Thanks for helping me out. However, I couldn't get the script to work. > Below > is the description. How does the t(sapply . script select the minimum > p-value? I understand that the split creates a list where e…

updated 15.6 years ago • Vincent J. Carey, Jr.

I really like the features that are provided in karyoploteR. https://bioconductor.org/packages/release/bioc/html/karyoploteR.html But, I am working with different organisms. I am able to find the organisms of interest using: > available.genomes() <code> [1] "BSgenome.Alyrata.JGI.v1"       &nbs…

software error R bsgenome karyoploter

updated 8.2 years ago • kirannbishwa01

<div class="preformatted">Hi Christoph- Are the aligned read files you are using actually in BED format (chr, start, end, name, score, strand)? I'll look into adding an option to allow a .dat extension as an alternative to .bed; if it is easy (and Gord has time...Hi Christoph- Are the aligned read files you are using actually in BED format (chr, start, end, name, score, strand)? I'll lo…

DiffBind DiffBind

updated 12.3 years ago • Rory Stark

test.rangedData, AnnotationData=Annotation) as.data.frame(annotatedPeak) <factor> <iranges> | <character> <character> <character> <numeric> <numeric> <character> MACS_peak_109 ENSMUSG00000089245 1 [54494876, 54496209] | MACS_peak_109...ENSMUSG00000089245 54826062 54826166 upstream numeric> <numeric> <chara…

miRNA GO BSgenome BSgenome ChIPpeakAnno miRNA GO BSgenome BSgenome ChIPpeakAnno

updated 13.4 years ago • Paolo Kunderfranco

test.rangedData, AnnotationData=Annotation) as.data.frame(annotatedPeak) * <factor> <iranges> | <character> <character> <character> <numeric> <numeric> <character> MACS_peak_109 ENSMUSG00000089245 1 [54494876, 54496209] | MACS_peak_109...ENSMUSG00000089245 54826062 54826166 upstream numeric> <numeric> <charac…

miRNA GO BSgenome BSgenome ChIPpeakAnno miRNA GO BSgenome BSgenome ChIPpeakAnno

updated 13.4 years ago • Paolo Kunderfranco

Prepare the 'metadata' data frame ... metadata: OK Now generating chrominfo from available sequence names. No chromosome length information is available. Warning messages: 1: In .deduceExonRankings(exs, format = "gff") : Infering...EXONID" "EXONNAME" "CDSID" "CDSNAME" > As a test, I would like to retrieve the transcript names for 3 Entrez Gene IDs. Note: I selected these 3 IDs randoml…

GO GenomicFeatures GO GenomicFeatures

updated 12.4 years ago • Guido Hooiveld

following shows that do.call of `c` on a list of IRangesList returns "list" only when the list is named. > library(IRanges) >example(IRangesList) > class(x) [1] "CompressedIRangesList" attr(,"package") [1] "IRanges" > class(do.call...c,list(x1=x,x2=x))) [1] "list" I am confused this. I would not expect the fact that the list is named to have any impact on the result…

updated 13.1 years ago • Malcolm Cook

Rcpp::List, Rcpp::List, int)’: integrate_build.cpp:29:42: error: call of overloaded ‘XPtr(Rcpp::Vector<19>::Proxy)’ is ambiguous PrebuiltXPtr curbuilt(prebuilt[r]); R version 4.2.2 (2022-10-31) Platform: x86_64-pc-linux-gnu

SimpleR

updated 2.9 years ago • cisbio

1.1056984 1.1096023 My question: Using annotation package how can I convert the probe ID's to Gene names. how do i incorporate gene name in place of 100_g_at? 2. How can I choose/filter P-values from T-test that are less than 0.01

Microarray Annotation Cancer annaffy convert Microarray Annotation Cancer annaffy convert

updated 21.4 years ago • James W. MacDonald

<div class="preformatted">> Hi Nathan, > > No, I never did get around to making a package for the remove > probes/probe sets functions, mostly because I don't know how! > I just used it again myself, and had to update the code slightly. The code > below works with R 2.7.2. As for how many probes you can remove, > there probably is no set ans…

cdf probe Biostrings cdf probe Biostrings

updated 17.3 years ago • lgautier@altern.org

<div class="preformatted"> I was expecting rd[ -1 , ] to be a RangedData object that contained all but the first row: > rd <- RangedData(IRanges(start=1:20,width=2),space=rep(letters[1:4],5)) > rd[['one']] <- 'one' > rd[1:2,] # OK RangedData with 2 rows and 1 value column across 4 spaces space ranges | one <character> <ira…

updated 15.9 years ago • Charles Berry

geneSelFunc, nodeSize=5, annot=annFUN.db, affyLib="hgu133plus2.db") where: - myAllGenes is a named vector of all p-values for each probe on the array, named after their probeID and - geneSelFunc is a function to select the

GO probe topGO GO probe topGO

updated 12.4 years ago • enricoferrero

or will this obscure the data? Just to be sure, here is my topGO code: where `` all_genes is my named vector of q values with entrez IDs as names. ````   `` <pre> GO_data_BP<-new("topGOdata",ontology="BP",allGenes=all_genes

topGO tophat kolmogorov-smirnov test

updated 8.5 years ago • aaronrosenstein

sample.id = as.character(sample_id[[1]]), : Nucleotide coded genotype should be 2 character string: line 1 Example 2: Perform my own SNP genotype coding and try again With a file like: 110043 rs2847443 3 1110059...File Line Accepted Rejected No call Skipped File name 1 9142000 0 0 9141999 0 0 ...er_line_coded.txt In the fi…

SNP snpMatrix SNP snpMatrix

updated 14.7 years ago • Chris K. Fuller

ranges strand | tx_id <rle> <iranges> <rle> | <character> ENSZALT00000030003 ARWJ01023036.1 21700-155713 + | ENSZALT00000030003 ENSZALT00000030004 ARWJ01023036.1...ENSZALT00000002808 tx_biotype tx_cds_seq_start tx_cds_seq_end <character> <integer> …

annotation ensembldb EnsDb AnnotationHub News

updated 6.1 years ago • Johannes Rainer

gt;>> Finding all hits in sequence chr1 ... >>> DONE searching Building feature vectors for scoring ... Calculating scores ... Annotating, filtering and generating reports ... Done annotating Add RE information...of 34 which is required for DeepCpf1 algorithm! ``` Summary.xls gives a NA for the sgRNA efficacy: ``` names forViewInUCSC extendedSequence gRNAeffic…

CRISPRseek

updated 3.5 years ago • Miguel

design) Error in makeContrasts(pivsmi = piRNA - miRNA, levels = design) : The levels must by syntactically valid names in R, see help(make.names). Non valid names: designputative miRNA,designsub scRNA,designvault

limma design and contrast matrix

updated 9.7 years ago • christopher.clarskon15

L17328" "S81916" "U63332" "M77235" and I would like to find ( in a repository for ex.) the names as: [1] "hypothetical protein LOC221823" [2] "meningioma (disrupted in balanced translocation) 1" [3] "fasciculation and elongation

proteinProfiles ProteomicsWorkflow ProteomicsAnnotationHubData Proteomics

updated 4.3 years ago • ALOK

<div class="preformatted"> >Date: Thu, 1 Dec 2005 18:44:24 +0100 >From: "Dr. D. P. Kreil" <dpkreil at="" gmail.com=""> >Subject: [BioC] limma: semi-bug (?) report for toptable >To: bioconductor at stat.math.ethz.ch > >Dear limma-maintainer, > >Firstly, thank you for providing limma, it has helped our work a lot. > >…

limma limma

updated 20.1 years ago • Gordon Smyth

enough sample names provided; using Sample1, Sample2, ... >> instead >> > > Hello Deepak, > > there is nothing in readCtData specifying...384 features, 16 samples > Feature types: Endogenous Control, Target > Feature names: Gene1 Gene2 Gene3 ... > Feature classes: > Feature categori…

Cancer cycle Cancer cycle

updated 15.6 years ago • Heidi Dvinge

library makeGRangesFromRefSNPids <- function(myids, verbose=FALSE) { ans_seqnames <- character(length(myids)) ans_seqnames[] <- "unknown" ans_locs <- integer(length(myids)) for (seqname in names(getSNPcount())) { if (verbose...gt; makeGRangesFromRefSNPids <- function(myids, verbose=FALSE) + { + ans_seqnames <- character(l…

SNP Annotation Cancer SNPlocs TranscriptDb GenomicFeatures GenomicRanges SNP Annotation

updated 13.9 years ago • SimonNoël

that does not recognize unidentified AA. I would like to replace the gaps '---' with an empty character '' during translation, somewhat similar to if.fuzzy.codon = 'solve'. Ideally I would also replace ambiguous codons...for (i in 1:50) { tryCatch({ aa = Biostrings::translate(orthologs[i], if.fuzzy.codon = "solve") name = names(orthologs)[i] cat(name, "N N 7 298 0.1", as.character(aa), "\n…

Translation Biostrings

updated 4.4 years ago • emmanuel.verde2939

ann.affy.go[[4]] An object of class "aafGO" [[1]] An object of class "aafGOItem" @id "GO:0000139" @name "Golgi membrane" @type "Cellular Component" @evid "IEA" [[2]] An object of class "aafGOItem" @id "GO:0003827" @name "alpha-1,3-mannosylglycoprotein...type "Molecular Function" @evid "IEA" [[3]] An object of class "aafGOItem" @id "GO:0006487" @name "protein amino acid N-linked glycosylat…

annaffy annaffy

updated 17.9 years ago • Ana Rodrigues

I am getting a segfault when trying to write a matrix of more than about 20 million character values each about 30 characters long.  The following demo reproduces the errors on my machine (edited to remove...matrix", c(nrow, ncol), size=100, level=0, chunk=c(min(nrow, 10000), min(ncol, 10000)), storage.mode = "character") h5write(test, file, "matrix") } hdfError()</pre> Afte…

rhdf5 segfault

updated 10.7 years ago • Kort, Eric

cds1 <- readRDS('example_cds.RDS') head(colData(cds1)) #shows annotations on each column as: cell (character), size factor (numeric), n.umi (numeric), perc_mitochondrial_umis (numeric), scrublet_score (numeric), scrublet_call...character), num_genes_expressed (integer) head(rowData(cds1)) #shows annotations on each row as: gene_short_name (character...id (character), chromosome (character)…

SingleCell AnnotationDbi

updated 3.3 years ago • techgirl2022

models that include extra exons for the retained introns and counted reads over them. I have named the retained introns so that they can be identified later. I know that when you build a DEXSeqDataSet, for each exon and...to subset the DEXSeqDataSet to only contain the retained introns with something like: dxd <- dxd\[vector\_of\_retained\_introns,\] However, I wonder if subsetting like…

dexseq

updated 10.5 years ago • i.sudbery

<div class="preformatted">Dear list members, again a stupid question: I wish to plot the results of hierarchical clustering with dendrograms and with heatmaps. I used the following functions: heatmap(exprs(data)[selected,]) and plot(hclust(dist(t(exprs(data)[selected,]), method = "euclidean"), method = "average")) The different arrays belong to different classes and I would like to lab…

updated 20.9 years ago • Heike Pospisil

download bigwig files for each sample of RNA-Seq data in GTEx via recount2. I can see bigwig file names defined for each sample (probably for each gene) in the 19th column through the following command. Then, how can I download...type %in% c("rse-gene", "rse-exon", "rse-jx", "rse-tx", "counts-gene", : 'match' requires vector arguments

recount

updated 6.4 years ago • hyp15

Dear BioC community, I have a boolean vector called `` pval `` where 1 means differentially expressed and 0 non-DE`` ,  ``whose element names are the Entrez IDs. In

topGO gene set analysis

updated 10.1 years ago • jacorvar

first data(twoGroups) #when I instantiate a DataTrack object: dTrack<- DataTrack(twoGroups,name="Uniform") #I got this error:Error in DataTrack(twoGroups, name = "Uniform") : #A chromosome must be specified for this annotation...track. #so I add a chromosome, which works fine... dTrack<- DataTrack(twoGroups,chromosome="chrX",name="Uniform") #the next error occurs when I try to plot …

Annotation Annotation

updated 13.4 years ago • Guest User

able to generate fold change vector for interesting samples but I have problem annotating eset. 6. I tried annotate the eset file using annotation from...table ID <- featureNames(eset) Symbol <- getSYMBOL(ID, "mogene10sttranscriptcluster.db") Name <- as.character(lookUp(ID, "mogene10sttranscriptcluster.db", "GENENAME")) tmp <- data.frame(ID=ID, Symbol=Symbol, Name…

Microarray Annotation annotate limma ASSIGN Microarray Annotation annotate limma ASSIGN

updated 11.5 years ago • Jakub Stanislaw Nowak

Hi folks, I'm interested in differential exon usage between genotypes in my RNAseq experiment. I've already aligned reads using HISAT2 on the Galaxy web platform, and now I'm trying to generate exon count tables for analysis using DEXSeq. As I'm a bioinformatics novice but have some very limited R experience, I've been using the work flows described in Appendix B of the Bioconductor DEXSeq docum…

rnaseq dexseq summarizedexperiment

updated 8.1 years ago • f.carlisle

IDs needed for Go Annotation, but they are not contained separately. Through my comparison, the names contain the EnsemblID within the peak IDs (Ex Conrol K9 Dy1-chr1_peak12171 ENSRNOG00000030145-Conrol K9 Dy3-chr1_peak22483...ID. I can do this using the right function in Excel =RIGHT(E2,18), since all Ensemble Ids are 18 characters. However, I would rather just complete this in R, by acces…

Annotation GO annotate PROcess Annotation GO annotate PROcess

updated 14.9 years ago • Julie Zhu

amp; 4+/IL2`) # or char2booleanFilter("4+/IFNg & 4+/TNFa & 4+/IL2") # takes a character as input which is more programmatic #then add to GatingSet, <span style="line-height:1.6">if name is not supplied, then...the entire expression string is used to name the new gate</span> add(gs, boolgate, parent="4+", name = "myBool") #compute the gate …

flowworkspace flow cytometry

updated 10.6 years ago • Jiang, Mike

Downloading: 240 B Downloading: 240 B Error: failed to load 'AnnotationHub' resource name: AH49186 title: Homo_sapiens.GRCh38.dna.toplevel.fa reason: 2 resources failed to download In addition: There were...warnings: <pre> 31: In curl::curl_fetch_disk(url, x$path, handle = handle) : progress callback must return boolean 32: In curl::curl_fetch_disk(url, x$path, h…

AnnotationHub

updated 10.1 years ago • Johannes Rainer

i="rpk")[,72574:145146] <- second_half_rpk #results. 'assay( <singlecellexperiment>, i="character", ...)' invalid subscript 'i' 'rpk' not in names(assays(<singlecellexperiment>)) ``` I obviously know that "'rpk' not in names(assays

SingleCellExperiment

updated 23 months ago • JalapenoCornbread

I have a bunch of transcript relative coordinates that I need to map to genomic coordinates. I am using a custom annotation file that I load using: txdb <- makeTxDbFromGFF(file='../2022_10_04_orthoalltime_novel_dge/ortho_alltime_merged_temp.gtf', dataSource="orthoalltime", organism="Homo sapiens", form…

GenomicFeatures

updated 3.2 years ago • nattzy94

things I learned. Every object in R has a class. However, some classes are more elementary (e.g. vectors, matrices, tables) and elements are extracted by giving the index (e.g. v[3], or m[1,4]). Many R functions return objects which...are lists. Components of a list can be extracted by name (list$mydata) or by component number (list[[3]]). Anything you extract also has a class. Most Biocond…

updated 21.8 years ago • Naomi Altman

div class="preformatted">Hello, I have 2 GRange objects gr1 and gr2 (with the same names but in a different order!) and I would like to "transport" the mcols of gr1 to gr2 - of course suitable for the names. Please ignore...IRanges data. The problem must be solved only via the names. gr1 GRanges with 5 ranges and 2 metadata columns: seqnames ranges strand | score…

IRanges IRanges

updated 12.7 years ago • Wim Kreinen

of another tibble not shown here. # create empty tibble tissue_sample_lists <- tibble( tissue = character(), sample_ids = list() ) # loop, and populate tibble tissues <- c('Duodenum', 'Ileum', 'Jejunum') for (x in tissues) { temp <- fastq_annotations_joined_cleaned...column and creating a new tibble with a loop, but it all seems very complex that I'm sure there must …

chromhmmData

updated 22 months ago • BioinfGuru

How to convert multiple protein fasta sequences into their gene/protein name

GenePrediction

updated 3.1 years ago • AROCKIYA

I'm using TopGo to do GO analyses. When I get my enriched terms, the long term names get corrupted. ```I have some text then ...```. For example: ``` GO:0000122 negative regulation of transcription by ... GO:0006886 intracellular...candidate_list_1[keep1] geneList1 <- factor(as.integer(bg_genes %in% candidate_list_final1)) names(geneList1) <- bg_genes GOdata1 <- n…

go software error topgo rna-seq

updated 5.6 years ago • morteza.aslanzadeh

<div class="preformatted">Hi All, I have a question about how to merge / have a union of 2 RangeData objects Say I have a rangeData1 head(rangeData1) RangedData with 6 rows and 0 value columns across 25 spaces space ranges | <character> <iranges> | 1 chr1 [ 101, 283] | 2 chr1 [ 704, 710] | 3 chr1 [ 310, 45…

updated 15.1 years ago • Vishal Thapar

RStudio, R and all packages downloaded and installed this week Following along with DIYtranscriptomics [https://diytranscriptomics.com/scripts][1] (lesson 1) which is superb (highly recommended), but I'm having issues. I know the key part of the error is `"attempt to set 'colnames' on an object with less than two dimensions"` but I don't know what that's referring to or what I can do to fix it. …

tximport

updated 4.6 years ago • bryce.thomas

Homo_sapiens data frame with 25 rows and 2 columns NCBI UCSC <character> <character> 1 1 chr1 2 2 chr2 3 3 chr3 4 4 chr4 5 5 chr5 ... ... ... 21 21 chr21 22 22 chr22 23 X chrX 24 Y chrY …

updated 12.7 years ago • Tim Triche

TRUE 46075 more elements ... @maPlate factor(0) Levels: @maControls factor(0) Levels: @maNotes character(0) @maGnames An object of class "marrayInfo" @maLabels [1] "1" "2" "3" "4" "5" 45691 more elements ... @maInfo Name Clone.ID X13834 13834...Cy5 SlideName 1 BC91_minusTS_Bio-6_RNAeasy_1 Stratagene_aT BC-D-091_aT shbg054 @maNotes character(0) @maNotes [1] "" 4. read.SMD() (…

updated 20.0 years ago • Wu, Zhuang

div class="preformatted">I missed this question. No, we have no plans to introduce use characters for chromosomes. Originally, this was decided based on some ideas of 1) reduced size in the database (not R) 2) better...Especially in light of the fact that you almost always have to do something with the chromosome names: different sources might be using chr01, chr1, ch01, ch1 etc. Kasper …

Genominator Genominator

updated 15.6 years ago • Kasper Daniel Hansen

0.995723495236492 NA And for these ensembl IDs I have got the gene name via a `biomaRt` query: > head(G_list) ensembl_gene_id hgnc_symbol ensembl_gene_id_version 1 ENSG00000007923 DNAJC11...How do I now alter `res` so that the results of my DE analysis display the gene name (as given in `G_list`) rather than the ensembl ID? I have tried to use `mer…

DESeq2

updated 5.1 years ago • Linda

<div class="preformatted"> I'm having trouble reading in my raw cel files and am unable to interpret the error message. Please see my error and code below. Last time I had to add varmetadata() info. and it worked, but that doesn't see to help in this case. Any suggestions will be appreciated. Thanks. Error: > OligoRaw = read.celfiles(filenames=list.celfiles(),phenoData=pd, verbose…

affy oligo arrayQualityMetrics a4 affy oligo arrayQualityMetrics a4

updated 12.0 years ago • Guest User

__moduleEigengenes()__.  I used __cbind() __\[or__ merge()__ \] function to combine the gene names and the module/color symbols. Although in this case the order of the rows is always the same, this seems not safe to me. The...dynamicMods) <span style="background-color:Yellow">genesMatchcolors <- cbind(dynamicColors, names(datExpr))</span> write.csv(genesMatchcol…

WGCNA cbind merge match gene names and Eigengene/module/colorlabels

updated 8.1 years ago • yifangt

testTrack) and I got the error: Error in IRanges:::.normargSEW(start, "start") : 'start' must be a vector of integers So I decided to troubleshoot it using simple examples. I used the following code: myseqs <- data.frame

BSgenome BSgenome BSgenome BSgenome

updated 15.8 years ago • sabrina.shao

background-color:Yellow">Pruning nodes...Error in read.table(file, dec = ".", sep = " ") : 'file' must be a character string or connection</span></pre>   I checked the file structures of mine and the results are below: &nbsp...230" "217" ... ..$ : chr [1:8] "Sample1" "Sample2" "Sample3" "Sample4" ... str(rankedList) Named num [1:5023] 0.84 0.129 0.915 0.95…

DEsubs error

updated 7.3 years ago • Talip Zengin

library('DESeq2') countMatrix = read.table("RPR_count.txt",header=T,sep='\t',check.names=F) dim(countMatrix) > head (countMatrix) HRPR_0D_V8_R1 LRPR_0D_V8_R1 HRPR_0D_V8_R2 LRPR_0D_V8_R2 1 ENSRNA049455608 27 15 13 20 2 ENSRNA049455955 50 31 66 20 …

deseq2

updated 6.7 years ago • nabiyogesh

<div class="preformatted"> Hi Dr.Carvalho, > ndf = read.table("100929_HG19_Deluxe_Prom_Meth_HX1.ndf", >stringsAsFactors=FALSE, sep='\t', header = TRUE) > head(ndf) PROBE_DESIGN_ID CONTAINER DESIGN_NOTE SELECTION_CRITERIA 1 537151_1_25 BLOCK1 interval rank target_tm:76.00;probe_tm:77.60;freq: 9.25;count:01;rules:0000;score:0812 2 537…

Annotation PROcess pdInfoBuilder charm Annotation PROcess pdInfoBuilder charm

updated 12.4 years ago • Nitesh Turaga

the openVignette help page. Error in setMethod("sampleNames", "Cel", function(object) object@name, : No existing definition for function "sampleNames" Error in library(affy) : .First.lib failed So, I tried to update pacakages...m1, where) : not an environment Error in setClass("AffyBatch", representation(cdfName = "character", nrow = "numeric", : Error in contained classes ("exp…

updated 22.2 years ago • Yasushi Okubo

deleted ] Patrick, I had a similar problem, and after some debugging I discovered that you must enter a valid groupName when calling BPMAPCelParser. You can get a list of the group names in the bpmap file by just looking

rMAT rMAT

updated 15.6 years ago • Larry Singh

iv) ploting functions for PCA and PLS - matchBox: The matchBox package enables comparing ranked vectors of features, merging multiple datasets, removing redundant features, using CAT-plots and Venn diagrams, and computing...1.29.5 (2012-06-19): - Added arrangeCelFilesByChipType() for moving CEL files to subdirectories named according to their chip types, which can be useful when for i…

BiocViews SNP Transcription Sequencing miRNA Microbiome Microarray qPCR Genetics Coverage

updated 13.3 years ago • Dan Tenenbaum

to annotate some rat data. When using the aafFunction in affaffy, all of the objects returned were "character(0)". I then tried the function using the example code from the help page. I was surprised to get the same result. Is there...6:10]) } Results: An object of class "aafList" [[1]] An object of class "aafFunction" character(0) [[2]] An object of class "aafFunction" character(0) [[3]…

GO hgu95av2 rat2302 Biobase annotate reposTools affy annaffy GO hgu95av2 rat2302 affy

updated 20.2 years ago • Kimpel, Mark W