Bioconductor Forum

package = "seqinr") cc<-read.fasta(file = dnafile) cc gives me then the following vector ... [47764] "t" "c" "c" "c" "t" ...... My problem is I would like now to use that vector to perform basic statistics eg; GC content analysis, base...frequencies . I hardly see how ? For instance an histogram on my vector like hist(cc) don't work My first intention by the way was to use biostring …

updated 16.2 years ago • m a

Saran, When you use scan("testdata.txt"), the data is not read in as a matrix. It is read in as a vector. Try class(data) or length(data) to see. You will need to convert the vector into a matrix. t.data<-matrix(scan("testdata.txt...data as follow: > data<-scan("testdata.txt") Then for cl argument, it is a vector containing the class labels of the s…

convert convert

updated 21.2 years ago • Aedin Culhane

and Covariate) In order to be able to set up the proper contrasts I split the Covariate in two Vectors where one Vector contains only the samples with the lowest level of the covariate e.g. CovBase = c(0,0,0,3,0,3,0,0) and where...the other vector contains all the samples with higher levels of the covariate e.g. Cov = c(34,2,5,0,5,0,2,34) and set up a design matrix without

limma limma

updated 12.4 years ago • Moritz Hess

How do you read a csv file that contains greek characters as part of the header (i.e. α, β etc) in R studio? Thanks

Greek

updated 9.5 years ago • Hem

QUERYID TXID <rle> <iranges> <rle> | <factor> <integer> <integer> <integer> <character> [1] chr1 109706393 + | intron 49314 49314 1 1785 [2] chr1 109706393 + | intron 49314 49314 1 1786 [3] chr1 109706393 + | intron 135483...1 7419…

VariantAnnotation locateVariant

updated 2.1 years ago • nhaus

ensembl_gene_id Length:259537 Length:259537 Length:259537 Class :character Class :character Class :character Mode :character Mode :character Mode :character …

DifferentialExpression TimeCourse timeOmics edgeR RNAseq

updated 20 months ago • Ashley

**12 Doctoral Candidates f/m/d Plant Proteomics, Bioinformatics and Biology** The opportunity: Plants are the nutritional basis of life on earth and protein-rich foods from plants are a global megatrend essential for sustaining an increasing human population and counteracting climate change. However, little is known about crop proteomes – the entirety of proteins that execute and control nearl…

JobPosting

updated 4.0 years ago • mengchen18

8674 9341 "VAMP5" "VAMP1" "VAMP2" "VAMP8" "VAMP4" "VAMP3" > grep("IL9R", s , value = T) named character(0) </pre>   <pre> > sessionInfo() R version 3.4.4 (2018-03-15) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu...file was construct from several sources: RefSeq, Ensembl, CCDS, Genecode, VEGA, dbSNP, CytoBand. The "Name" column of the…

homo.sapiens

updated 7.4 years ago • Vang Le

lt;< Following Factors in your pd(sample_sheet.csv) will be analysised: >> <id>(character):treatment1,treatment2,control <plateindex>(character):Plate 01, Plate 02 <welladdressindex>(character):B01, C01, D01...0.45, -0.44, -0.42, -0.40, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85 <type>(character):treatment1,treatment2,contro…

methylationArrayAnalysis EPICarray ChAMP Champ.SVD

updated 4.8 years ago • arisarkar88

I need to edit the fragment IDs in a MiSeq fastq file. I'm using ShortRead to load the fastq and I've successfully managed to insert the substring needed  but I can't use my code to substitute the new ID into the id slot of my fastq.  Here is my current code: fqr <- sub(" ",barcodestr, ShortRead::id(fqr)) In this case, the result is a list with only th…

ShortRead

updated 11.0 years ago • newmanss

<div class="preformatted"> I am interested in analysing the differential expression of the transcriptome of A.flavus grown at two different condition using easyRNASeq and DEGSeq. I have the raw reads in fastq format for the expt. I had mapped these reads to the reference genome sequence using bowtie and the output bam file was given as input to easyRNASeq. It gave the error ".doBasicCoun…

Annotation Organism DEGseq easyRNASeq Annotation Organism DEGseq easyRNASeq

updated 13.0 years ago • Guest User

a publication[1] that looks like this: http://cbio.mskcc.org/~lianos/images/barfig.png I have some vectors with "scores" (that you see is plotted horizontally there) that I'd just like to turn into some colored representation...darkred'))(30) plot(1, 1, xlim=c(0, 50), ylim=c(-1,1), type="n", axes=FALSE, bty="n", xlab=names(scores), ylab="") rect(xlef=0:nboxes, ybottom=1, xright=(0:nboxes)+1, yto…

Biophysics Biophysics

updated 17.6 years ago • Steve Lianoglou

much trivial! It is the problem with the quotation, in >getProbePackage(disdiv712aprobe), the name of the probe package should be quoted! :-( O.K, now, following each step in compute.affinities, I finally came to the "real" problem...pmIndex[subIndex]] = apm Error: NAs are not allowed in subscripted assignments I have checked vector "apm" and there is no NA, and the lengths of apm and tm…

Microarray Cancer probe gcrma ASSIGN Microarray Cancer probe gcrma ASSIGN

updated 20.8 years ago • Wenqiong Chen

div class="preformatted">Hello, I have a fastq file compressed with gzip in a directory named test/. I would like to assess its quality. Here is what I do: $ R > library(ShortRead) > qa <- qa("~/test", "fastq.gz") > report(qa, dest...for function 'as.data.frame': Error in FUN(X[[1L]], ...) : invalid format '%.3g'; use format %s for character objects Here are more…

updated 11.3 years ago • TimothéeFlutre

Hi all, I am trying to construct a gene track using TxDb. Hsapiens.UCSC.hg19.knownGene in Gviz package. I found a region that does not return any gene while when I look up in the TxDb there is actually transcripts.  Please see the following code that I used: library(Gviz) library(GenomicRanges) library(TxDb.Hsapiens.UCSC.hg19.knownGene) library(org.H…

txdb txdb.hsapiens.ucsc.hg19.knowngene gviz

updated 8.3 years ago • izzy.yichao.cai

I extract the contrast results to get the site M vs site K when gender is Female with the contrast vector, I found that some of the all zero contrasts are not properly filtered.  I debug the code using RStudio and find that...in CleanContrast function , when a numeric contrast vector is used, contrastAllZero <- contrastAllZeroNumeric(object, contrast) is called. If I get the logic…

software error bugs deseq2

updated 10.0 years ago • john.hu

to find an inherited method for function ‘getListElement’ for signature ‘"IRanges"’ > as(dat,'vector') Error in as.vector(from) : no method for coercing this S4 class to a vector > as(dat,'integer') Error in as.vector(x, mode = "integer...no method for coercing this S4 class to a vector</pre>   <pre> > sessionInfo() R version 3.5.0 (2018-04-23…

iranges

updated 7.7 years ago • li lilingdu

Tree L1 Ctrl 3hrs 24hrs 48hrs Tree L2 Ctrl 3hrs 24hrs 48hrs I have assigned 2 factor vectors as: "tree" --> vector for the trees. "trtTime" --> vector for the control and after treatment time. I would like to study which

ASSIGN ASSIGN

updated 13.6 years ago • KJ Lim

the samr package. I have an excel sheet with 25 columns and 22811 lines. the first row has the names of the experiments and the first column contains the names of the genes. I saved this file to a tab-delimited table and...with and without the header. >test_TS <- read.table("test_data_TS.txt" ) #constructing the vector >y=paste(c(rep(1,12),rep(2,12)),"Time",rep(c(1,24,3,48,6…

convert convert

updated 16.8 years ago • Assa Yeroslaviz

e) Error in .C(twins, n, jp, as.double(x2), dv, dis = double(if (C.keep.diss) length(dv) else 1), : 'name' must be a string (of length 1) or native symbol reference Could anyone point me to the right direction on to how to fix this

Microarray GO Clustering adSplit Microarray GO Clustering adSplit

updated 13.7 years ago • Luz Mayela Soto

When I get to 4, I get the following: <pre> data <- matrix(0,15,10) itemLabels <- vector("character",15) data[1:5,] <- 1 ; itemLabels[1:5] <- "a" data[6:10,] <- 2 ; itemLabels[6:10] <- "b" data[11:15,] <- 3 ; itemLabels[11:15] <- "c" data[1,1

bhc

updated 10.7 years ago • b.curran

paste("Something went wrong parsing:", class, id, ". Parsed ", : cannot coerce type 'closure' to vector of type 'character' In addition: Warning message: In internal_getBiopaxModelAsDataFrame(ret, biopaxxml, verbose = verbose

rBiopaxParser rBiopaxParser

updated 12.6 years ago • suzy.stiegelmeyer@syngenta.com

<div class="preformatted">Hello, I am trying to read an Illumina final format .txt file (tab-delimited) into snpStats. The file contains 4 columns: snp, sample, allele 1, and allele 2. Some sample lines: BICF2G630100019 04-0677/J279 C C BICF2G630100032 04-0677/J279 T T BICF2G630100034 04-0677/J279 G G BICF2G630100043 04-0677/J279 A A BICF2G630100054 04-…

SNP Genetics snpStats SNP Genetics snpStats

updated 13.9 years ago • Liz Hare

line-height:1.6">My question is if I can use sva, if the variable of interest is matrix instead of a vector? In all the exaples I saw variable of interest was always a vector like cancer status, etc..    Thanks!</span>   &nbsp

sva variable of ineterest matrix

updated 9.1 years ago • reyhan.sonmez

Hi, I am trying to build a model for DESeq2 analyses. In past I have done simpler version of analyses where the model was not so complicated. I have few questions and I will sincerely appreciate if someone from his/her experience can answer them (ofcourse the answers from Micheal Love are very Welcome). So I have a metadata that has Gender (M/F), BMI(H/OB), AGE(Y/O), DiseaseScore(I/S) STATUS(DR…

DESeq2

updated 2.5 years ago • Abhishek Singh

xist_pos) > filter(T_Singlets_MyFlowSet[[29]], xist_pos) A filterResult produced by the filter named '' #<-****It doesn´t recognize that the name of the gate is xist_pos > result3 = filter(T_Singlets_MyFlowSet[[29]], xist_pos) #there...that does not return me the result statistics > result3 A filterResult produced by the filter named '' > summary(result…

flowCore openCyto Summary Result Filter

updated 5.7 years ago • noviello

chromosome="chr5", genome="hg19", >>rstart="exonStarts", rends="exonEnds", gene="name", symbol="name2", >>transcript="name", strand="strand", name="RefSeq Genes", feature="name2", >>showId=T, from=122428653, to=122432628...to=122432628) >>Error in unit(rep(1, n), "strwidth", data = data) : >> 'x' and 'units' must have length &…

updated 13.4 years ago • florian.hahne@novartis.com

Is there any way to add an asterisk (or another character) at the outside of a circular tree in order to annotate/highlight specific taxa/tips in the tree

ggtree

updated 6.7 years ago • alisa.postma

the Taffy example in the docs I receive the following error with acc2LLMapper: =20 =20 Error in "names<-.default"(*tmp*, value =3D c(byID, id)): Names attribute must be the same length as the vector =20 =20 Any ideas? =20 Thanks =20 Barry...charset="utf-8" content='3D"text/html;' http-equiv="3DContent-Type"/> <meta content="3DWord.Document" name="3DProgId"/> <meta 10"="" conten…

AnnBuilder AnnBuilder

updated 23.5 years ago • Barry Henderson

bioconductor I am posting a bug report here. The problem is import function calls parseURI on file names: <pre> library(rtracklayer) import.bed("my bed file.bed") <span style="background-color:Yellow">Error in parseURI(uri) : cannot

software error rtracklayer

updated 10.4 years ago • balwierz

ranges strand | V4 V5 ## <rle> <iranges> <rle> | <character> <numeric> ## [1] chr1 815093-817883 * | MACS_peak_1 295.76 ## [2] chr1 1243288-1244338 * | MACS_peak_2 63.19 ## [3] chr1 2979977-2981228...could you tell me why is there a * under the strand column instea…

ChIPseeker

updated 4.6 years ago • Meghna

CN <rle> <iranges> <rle> | <factor> <numeric> <numeric> <character> [1] 1 422501-424500 * | SRR1945750_map_to_pan.sort.bam -5.32162981450578 -4.24086714482953 CN0 [2] 1 549001-551000...clear to me. Thanks! [1]: https://github.com/Bioconductor/copy-num…

cn.MOPS CNV copy number

updated 5.9 years ago • liorglic

<div class="preformatted"> I am having problems reformatting my data. My data has several samples on one plate, so I am reading in using the format = "plain" options, and then calling changeCtLayout() to reformat it. I am reading in a 96 well plate that is organized as a 1x84 matrix (several wells not used). For the sake of detail I will be very verbose, and the first few lines of my file…

a4 a4

updated 13.1 years ago • Guest User

The results are a table with several annotations and custom measure of significance. I've created a named vector (list) containing all the genes present in the array (ensembl IDs) with the corresponding measure of significance...geneList. geneList <- abs(data[ ,2]) names(geneList) <- data[ ,1] geneList[1:5] ENSMUSG00000025903 ENSMUSG00000025903 ENSMUSG00000025903 ENSMUSG00000025903…

Genetics Annotation GO hgu95av2 convert biomaRt topGO Genetics Annotation GO hgu95av2

updated 13.8 years ago • António Miguel de Jesus Domingues

div class="preformatted">Hi Axel, Thanks for pointing out the error in the way I was specifying the "names" field (names= targets[,"Names"]). My targets file actually has 8 rows (8 files). Initially I had some other problem reading them...there was an error in the file names), so I started working with only one file. But I was not careful enough during copy-pasting and pasted names= targets[,…

Annotation GO limma Annotation GO limma

updated 14.9 years ago • Hari Easwaran

metadata(0): assays(2): Green Red rownames(574981): 10600322 10600328 ... 74810485 74810492 rowData names(0): colnames(1735): 6057833166_R02C02 6057833166_R04C02 ... GSM4199991_202226400157_R07C01 GSM4199992_202226400157_R08C01...colData names(1): ArrayTypes Annotation array: IlluminaHumanMethylation450k annotation: ilmn12.hg19 > rgSetEPIC class: RGChannelSet...metadata(0): assays(2…

RGset combinearrays 450k minfi

updated 4.4 years ago • Sophie Marion de Proce

being arranged in folders by site. # Within each species folder, there should be two folders, one named "Sample" containing all samples for that species # And the other named "Blank" containing all blanks for that species. # Create...vector with all sites you wish to analyze sites <- c("Tiputini","Yasuni") ####### Loop through directories containing .mzXML files. Samples...and their assoc…

xcms memory findchrompeaks

updated 4.8 years ago • abrsoule

set of bins in a GrangesList, and a set of regions I would like to mask. My goal is to get a list of vectors, where each vector indicates the fractions of the bins not overlapped with the masked regions, so I can use these vectors...lt;- GenomicRanges::width(ovr_intersect) / bin_size # Convert the overlap fractions into vectors ovr_val_ls <- base::split(ovr_val, names(ovr_val)) …

IRanges GenomicRanges

updated 4.7 years ago • Yixin

Hi! My name is Enrique Pérez. I need help because I have been trying to run GSA() function, but I have had the next error all the time: <pre...x=x[,-1] y=as.numeric(c(rep(1,dim(x)[2]/2), rep(2,dim(x)[2]/2))) genenames=rownames(x) genesets=vector("list",50) for(i in 1:50){ genesets[[i]]=sample(rownames(x),size=30) } x.gsa=GSA(x, y, genenames = genenames, genesets = genesets, resp.type.…

GSA

updated 9.0 years ago • epercamh

annot=???,affyLib=???)</pre> __Q2.1__-The geneList parameter should contain a vector whose names are all the cpg markers on the chip (or genes) with p-values calculated from lme4, correct? __Q2.2__-The geneSel...parameter should contain a boolean vector of the cpg markers (or genes) whose p-value is below the alpha threshold, correct? __Q2.3__-My other question is related

topGO illuminahumanmethylation450k.db

updated 7.9 years ago • dusan.petrovic

issue but when try to get the output analyzed I am receiving an error "Error: cannot allocate vector of size 188.5 Mb" on a maching that has 2.0 GB of RAM. Any suggestions? Thanks Louisa Rispoli > library(bgx) Loading required...eta: 0.1 *** Adaptive MCMC: 1 *** Batch size: 50 *** Optimal acceptance ratio: 0.44 *** Name of output directory: ./run.3 *** Seed for rando…

probe probe

updated 18.0 years ago • Louisa A Rispoli/AS/EXP/UTIA

_tx_id), FOREIGN KEY (_tx_id) REFERENCES transcript ); CREATE TABLE `metadata` ( `name` TEXT, `value` TEXT ); However, one important field seems to be missing: CDS phase. Phase specifies how many nucleotides must...exon_rank #> <Rle> <IRanges> <Rle> | <integer> <c…

GenomicFeatures phase gene models GFF

updated 8.2 years ago • arendsee

of the "names" are Entrez Gene IDs) that are in category GO:0006836, and 4 of entries I have marked as significant by setting their values...lt;- list() test.stat.BP[1] <- list(new("classicCount", testStatistic = GOFisherTest, name = "Fisher test")) result.BP[1] <- list(getSigGroups(BP.GOdata, test.stat.BP[[1]])) test.stat.BP[2] <- list(new("elimCount", test…

GO hgu133plus2 annotate geneplotter graph Rgraphviz PROcess goTools biomaRt Category GO

updated 18.4 years ago • Dick Beyer

in the UniProt database. To be specific; among others I would like to retrieve the preferred gene name, which is labeled "Gene names (primary)" in the resulting table when using UniProt's web-based ID mapping interface. As example...29%2Cyourlist%28M2015022613L2TBUNHS%29) As can be seen, this ID links to multiple (13) gene names/synonyms (7th column), but the primary gene name is Psmb9 (5th co…

uniprot.ws uniprot

updated 10.9 years ago • Guido Hooiveld

mcols(resctrst2) DataFrame with 6 rows and 2 columns type description <character> <character> 1 intermediate the base mean over all rows 2 results log2 fold change: time 12 vs 6 3 results standard error...results BH adjusted p-values -- Sent via the guest posting facility at bioconductor.org. </character></charact…

updated 11.8 years ago • Guest User

and par(mai=c(2,0.82,0.82,6)) still no luck. Don't know how to go about getting the full Gene names displayed on the tree. Thanks in advance, Alan sessionInfo() R version 3.2.2 Patched (2015-08-16 r69094) Platform: x86\_64

ggtree

updated 10.3 years ago • Alan Smith

first category.__ To get the right gene mappings, I did this, where __diff\_exp\_ensembl is just a named vector containing genes and 1 or 0 depending on whether it is differentially expressed or not__: <pre> go2gene = getBM(attributes...c("ensembl_gene_id", "mgi_symbol", "go_id"), mart = mouse) ## map from gene name to ensembl go2gene = go2gene[which(go2gene$ensembl_gene_id %in% names(d…

goseq gene ontology biomart annotate category

updated 8.5 years ago • krc3004

Hello, I am trying to complete a sequence search using RNA-seq reads with the Biostrings function vcountPDict. However, I am running into out-of-memory errors when running vcountPDict() and I'm looking for some guidance with 1) my implementation may not be optimal or 2) what are typically the largest number of sequences in PDict object one can search for? Background: I have 4,722 50b…

software error Biostrings

updated 5.3 years ago • jennyl.smith12

When subsetting a qPCRset (e.g., for features), the sample names get lost. Assigning an expression set explicitly does not work as well. Let's say _raw_ is a qPCRset: <pre> rawSub <- raw[myFeatures

HTqPCR

updated 9.0 years ago • henrik.seidel

nbsp; I apologise for all the questions, but I have two more!   1) Is there a way to get gene names on the "peaklist" object obtained from the findOverlapOfPeaks function? I'm able to get the peaklist but it's just a very

chippeakanno overlappingpeaks annotation

updated 9.1 years ago • jmKeith

strand | tx_id tx_name <rle> <iranges> <rle> | <integer> <character> ENST00000456328.2 chr1 9869-12068 + | 1 ENST00000456328.2 ENST00000450305.2 chr1 10010-12209 + | 2 ENST00000450305.2...seqinfo: 640 sequences (1 circular) from hg38 genome > 9869-12068 [1] -2199 # this is not 2000 `…

TxDb.Hsapiens.UCSC.hg38.knownGene

updated 12 months ago • linouhao

<div class="preformatted">Paolo, Just to let you know that starting with ChIPpeakAnno 2.5.11, you can pass a mart object to addGeneIDs instead of orgAnn. Thanks for your input! Best regards, Julie On 7/30/12 4:51 AM, "Paolo Kunderfranco" <paolo.kunderfranco at="" gmail.com=""> wrote: > Hello, > Ok perfect now is working fine, > Thanks again for your precious …

miRNA Annotation GO BSgenome biomaRt BSgenome ChIPpeakAnno miRNA Annotation GO BSgenome

updated 13.4 years ago • Julie Zhu

<div class="preformatted">Hello- I have Affymetrix .cel files that I have read into R using the affy package. I am able to do normalization, transformation, and even cluster analysis. I cannot figure out how to do gene filtering operations-how do I tell R which samples I am interested in comparing to which other samples? I have two duplicate experiments that are vector controls, two dup…

Normalization Normalization

updated 23.1 years ago • Michael Benjamin

coding\_gene\_flank" from the current human ensembl assembly and whether I provide just one ENSG name or a vector of 1000s, whether I ask for 100 or 2000 upstream or downstream bps, regardless of my request, I get a query error

biomaRt Query ERROR biomart Filter upstream_flank NOT FOUND

updated 9.7 years ago • Ddaubentonia

filename.dots -Tpng -o filename.png" in dos windows. The png picture would display the Chinese characters correctly. But the same trick seems failed in Rgraphviz. >library(Rgraphviz) >set.seed(123) >V <- paste(letters...collapsed again. WIth the following codes, there is no error, but the label displayed with stranged characters instead of Chinese charaters. &…

Rgraphviz Rgraphviz

updated 16.3 years ago • Michael

RQ1_sorted) 1 2 5 3 4 1484 1430 104 0 0 > RQ1_df <- data.frame(word = names(RQ1_sorted), freq = RQ1_sorted) > head(RQ1_df) word freq 1 1 1484 2 2 1430 5 5 104 3 3 0 4 4 0 > findFreqTerms(RQ1_tdm, lowfreq...50) character(0) > findAssocs(RQ1_tdm, c("digital"), corlimit=0.85) $digital abstr…

dendrogram hclust textanalysis R RStudio

updated 4.7 years ago • Abby

is.character(type)) { i = match(type, CURLcodeValues) typeName = if (is.na(i)) character() else names(CURLcodeValues)[i] } typeName = gsub("^CURLE_", "", typeName) fun = (if (asError) stop else warning) fun(structure(list

updated 13.3 years ago • Guest User

<div class="preformatted">Hi I seem to be getting an error when trying to replicate ReportingTools example of putting a plot on the webpage both using the one generated in R and an external image. Not sure if the error has anything to do with versions. Session info included too. ### #plot generated within R ### my.df <- data.frame(EGID = c("103", "104", "105", "106", "107"), …

GO GO

updated 12.6 years ago • Abhishek Pratap

title type source_name_ch1 GSM424759 pSUPER-scramble replicate 1 RNA HUVEC infected by retroviral vectors bearing a control scramble sequence GSM424760 pSUPER-scramble replicate 2 RNA HUVEC infected by retroviral vectors...a control scramble sequence GSM424761 pSUPER-scramble replicate 3 RNA HUVEC infected by retroviral vectors bearing a control scramble sequence GSM424762 pSUPER-mir-210 repl…

updated 14.4 years ago • Jing Huang

ensembl entrez hgnc_symbol chromosome band <character> <integer> <character> <character> <character> ENSG00000150361 ENSG00000150361 57626 KLHL1...nbsp;             &…

deseq2

updated 7.9 years ago • jarod_v6@libero.it