Bioconductor Forum

<div class="preformatted">Hi, Hope you're fine I am trying to make whole genome plots using the geneplotter package/annotate package. The organism I am studying is Arabidopsis thaliana, and obviously the annotations are not so extensive there: when trying to build a chromLocation object, I can't obviously do that (see error below) It is obvious to me, that the chromosome location mappings…

Organism ath1121501 Organism ath1121501

updated 17.2 years ago • Samuel Wuest

<div class="preformatted">Hello, Is there a neater way to import an entire chromosome ? uniqueness <- import("mapabilityAlign36mer.bigWig", which = GRanges("chr5", IRanges(1, end = .Machine$integer.max - 1...div class="preformatted">Hello, Is there a neater way to import an entire chromosome ? uniqueness <- import("mapabilityAlign36mer.bigWig", which = GRanges("chr5", I…

updated 11.8 years ago • Dario Strbenac

gtf prints out an extremely long list of errors like the ones below: ``` ERROR: Unable to find chromosome 'hg38_knownGene_ENST00000407684.1' in the SAM header! ERROR: Unable to find chromosome 'hg38_knownGene_ENST00000401533.7...in the SAM header! ERROR: Unable to find chromosome 'hg38_knownGene_ENST00000474095.1' in the SAM header! ERROR: Unable to find chromosome 'hg38_knownGene_ENS…

RNASeq featureCounts

updated 4.4 years ago • nklier38

per patient, I was trying to annotate some selected CNAs with their respective total copy number, to obtain the relevant annotated genes; On this premise, I tried to use the CNVRanger R package and proceed as follows...r head(ex.dt) # the input data frame of selected copy number annotations based on hg19 reference # A tibble: 6 x 5 chromosome start end state file <…

CopyNumberVariation CNVRanger GenomicRanges

updated 3.9 years ago • svlachavas

<div class="preformatted">Hi, I currently have a list of HUGO gene ids which relate to genes in areas of gain over a whole chromosome, and would like to perform GO enrichment analysis on them. So I have 2 problems: 1. currently i have been defining my...Hi, I currently have a list of HUGO gene ids which relate to genes in areas of gain over a whole chromosome, and would like to perform G…

Annotation GO Annotation GO

updated 17.3 years ago • Nathan Harmston

downstream analyses (using CAGEr), the reads aligning on the viral sequences are ignored because the chromosome name is not in \`seqnames(BSgenome.Hsapiens.UCSC.hg38)\`.  I am thinking of adding the viral sequences to the

bsgenome virus

updated 9.3 years ago • Charles Plessy

Hi, I want to remove X and Y chromosome genes from my bulk seq data. I don't know how to proceed with that. Do I need to remove the genes from the counts after...and I am not getting any error in that. I think is am not using it correctly for removing Xand Y chromosome genes. Any help is appreciated. Thanks ``` dds[ all(!seqnames(dds) %in% c("chrX", "chrY

DESeq2 RNASeq

updated 5.0 years ago • Archit

a set of SNV, CNV, SV from cancer samples 2 -- we would like to display the SNV and CNV along the chromosomes (on the linear scale, ie. HORIZONTALLY) 3 -- we would like to display the SV, especially TRANSLOCATIONS, as VERTICAL...LINES connecting the breakpoints on the chromosomes that are represented HORIZONTALLY thank you very much, -- bogdan       &nbsp

ggviz ggplot2 gviz circlize Rcircos

updated 7.4 years ago • Bogdan

div class="preformatted">Dear all, I would like to represent 2 (chromosomal) interactions as Granges data structure: let's say : chr1 1000-1010 site interacting with chr1 5000-5010 chr1 5000

ggbio ggbio

updated 13.4 years ago • Bogdan

Dear all, I want to find out on which Chromosome a Gene is. I am trying to adapt below code which uses the Gene Entrez to get the Chromosome Location. I already have...Bimap interface: x <- org.Hs.egCHR # Get the entrez gene identifiers that are mapped to a chromosome mapped_genes <- mappedkeys(x) # Convert to a list xx <- as.list(x[mapped_genes]) if(length(xx) > 0) …

org.Hs.egCHR org.Hs.eg.db

updated 5.1 years ago • Bine

see 1st chromosomes head(seqlengths(mf_genome)) # see how many base pairs are in chromosome 1 mf_genome[["1"]] # chromosome 1 had 223606306...na> <na> <na> # CM021958.1 <na> <na> <na> # CM021959.1 <na> <na> <na> # see 1st chromosomes head(seqlengths(new_genome)) # CM021939.1 CM021940.1 CM021941.1 CM021942.1 CM021943.1 CM021944.1…

BSgenome.Mfascicularis.NCBI.6.0

updated 10 months ago • Genevieve

Hello, guys,   I used Gviz for plotting human genome chromosome ideogram in one picture together, but when I get the picture, I find the width of each chromosome is similar, for example

Gviz chromosome ideogram

updated 8.8 years ago • dulunar

div class="preformatted">Hi, Is there any tool or package that takes chromosomal ranges (instead of gene IDs) as input and performs GO analysis? Any help will be appreciated. --Yadav [[alternative

GO GO

updated 13.6 years ago • Yadav Sapkota

<div class="preformatted"> Dear list, Im struggling retrieving the full list of the entrez geneIDs for each of the enriched chromosome bands (obtained by "GOstats"). revmap(org.Hs.egCHR) doesnt give the entrezIDs for the sub-arms, only for the whole arm...Dear list, Im struggling retrieving the full list of the entrez geneIDs for each of the enriched chromosome bands (obtained by "GOstat…

updated 15.3 years ago • Xi Zhao

tools_2.6.1 # # #Define Functions # #plot a graph whose edges are all in a second graph (template) plotGraphWithTemplate = function(g1,template,...){ e1 = edgeNames(g1); e2 = edgeNames(template); indexMatchingEdges = is.element...e2,e1); for(i in which(!indexMatchingEdges)){ template at AgEdge[[i]]@color="transparent"; } for(i in w…

Cancer graph Rgraphviz Cancer graph Rgraphviz

updated 17.9 years ago • Rand, Hugh

div class="preformatted">Hi, is there any standard assigning an integer index to the mitochondrial chromosome just like we assign 23 and 24 to ChrX and ChrY? I need to pick an integer for my internal encoding and I prefer to stick

ASSIGN ASSIGN

updated 17.6 years ago • Henrik Bengtsson

Using the quant smooth package to retrieve chromosome lengths produces this size for chromosome 18 (as example, others are also different): 76117153 however, both...ensemble and ncbi give a value over 80 mbp for that chromosome. I used this command: <pre> chrlen<-lengthChromosome(chroms[i],"bases") print(paste("processing chrom ",chroms[i]," (",chrlen...c(-2,nrow…

quantsmooth

updated 11.2 years ago • bob.stephens.2005

div class="preformatted">Dear All I am trying to make a nice line chart using subset of my eset. I have been trying all night but I did not get very far, it does not seem to be as popular as other...charts in Bioconductor literature. I just could not find any examples. Can anyone help me with this? Which package to use and

updated 13.8 years ago • Dana.Stanley@csiro.au

needs the 'which' paremeter, which needs a GRanges object. Is there an easy way to, say, get all chromosomes from a file (not contigs)? And since it seems to require an IRanges object for the 'ranges' parameter of the GRanges...object, is there an easy way to simply get all the data from each chromosome? Or do I have to find then plug in the coordinates for each chromosome?   Thank y…

GRanges IRanges

updated 9.3 years ago • Kyle Johnsen

<div class="preformatted">On Tue, Oct 28, 2008 at 2:59 AM, Sean Davis <sdavis2@mail.nih.gov> wrote: > On Mon, Oct 27, 2008 at 9:13 PM, Steve Lianoglou > <mailinglist.honeypot@gmail.com> wrote: > > Hi, > > > > On Oct 27, 2008, at 6:39 PM, Camper (Chih-Wei Liu) wrote: > > > >> Hi all, &…

miRNA ideogram GenomeGraphs rtracklayer microRNA miRNA ideogram GenomeGraphs rtracklayer

updated 17.2 years ago • Michael Lawrence

lt;- predictCoding(vcf, txdb, seqSource=Athaliana)" to detect coding SNPs. The problem is that the chromosome names are not consistent among VCF, txdb and BSgenome. In vcf, the chromosome name is "Chr*", in txdb, the chr name is "Chr...in BSgenome, the chr name is "chr*" . I know I can use renameSeqlevels() to adjust the seqlevels (chromosome names) of the VCF object to match that of the txdb an…

Annotation BSgenome BSgenome Annotation BSgenome BSgenome

updated 13.3 years ago • sun

if (and this is a common situation) I have multiple gene ids in my dataset with the same E.C number, how does Pathview assign a colour/value to this E.C number in the final figure?   thanks

pathview

updated 9.3 years ago • devang3110

I have chromosomal location or genome coordinates for list of miRNAs. Please advice me how can I make a figure to better visualize

cancer

updated 6.6 years ago • angajalaanusha

having trouble plotting an alignment track from sequence data that was aligned to hg19 with non-UCSC chromosome names (i.e. "1", not "chr1"). I _suspect_ the problem is to do with the chromosome names, but I am not sure. My code...subRegion), x@args, x@mapping) 7: .local(x, ...) 6: subset(x, from = from, to = to, chromosome = chromosome, sort = FALSE, stacks …

gviz software error

updated 7.3 years ago • laura.k.hilton

inst/doc/derfinder-quickstart.html) for `` derfinder `` running the analysis for an individual chromosome: fullCov <- fullCoverage(files = files, chrs = 'chr21', verbose = FALSE) ## Get the region matrix of Expressed Regions (ERs...This is all very straightforward and clear, but it means doing the analysis for each individual chromosome, which might be a good idea for…

derfinder recount

updated 8.1 years ago • António Miguel de Jesus Domingues

How can I increase the distance between the chromosomes plotted? when all the chromosomes are plotted with their data backgrounds ? currently everything is so jam packed

karyoploteR

updated 6.7 years ago • saeed Ur Rehman

Dear Gunter, please if I may add another 1-2 questions : after running cn.MOPS per chromosome on a PBS computer cluster, sometimes, in the output it says : <pre> "No CNVs detected. Try changing "normalization", "priorImpact...Dear Gunter, please if I may add another 1-2 questions : after running cn.MOPS per chromosome on a PBS computer cluster, sometimes, in the output it says : <pr…

cn.mops referencecn.mops

updated 8.7 years ago • Bogdan

Can anyone tell me how to run eBayes to compare two subsets of samples (with and without monosomy of chromosome 10) using only probesets mapped to chromosome 10? Thanks. Dr. Martin G. McCabe Cancer Research UK Clinical Research

affy affy

updated 17.4 years ago • Martin McCabe

are generated fine with ' chromosome = "chrX" ' Thanks a lot for any help! Best, Martin Sample code: library(Gviz) #regions with genes st=17740000 ed=17750000...bmTrack <- BiomartGeneRegionTrack(start=st, end=ed, chromosome="chrX", genome="hg19",showId = TRUE,background.title = "white", name="",fontsize=20,col="black")…

Annotation Gviz Annotation Gviz

updated 12.5 years ago • Martin Rijlaarsdam

Hi,   How can I find the nucleotides, given the chromosome and the genomic positions? I was trying to use the Biostrings package, but couldn't find the function that would

biostrings

updated 11.2 years ago • Brian Smith

analysis?  I know there are scaling factors, β-actin and GAPDH, percent present,NUSE box chart and RLE box chart . But there have specific standards for the NUSE line drawings and the RLE box drawings, for example&nbsp

affy

updated 8.3 years ago • llkxiaolan

read_maq_map.cc:149: error: there are no arguments to 'new_RoSeqs_from_CharAEAE' that depend on a template parameter, so a declaration of 'new_RoSeqs_from_CharAEAE' must be available read_maq_map.cc:149: error: (if you...read_maq_map.cc:150: error: there are no arguments to 'new_XStringSet_from_RoSeqs' that depend on a template parameter, so a declaration of 'new_XStringSet_from_RoSeqs' must be a…

ShortRead Rsamtools ShortRead Rsamtools

updated 15.2 years ago • Bernt Guldbrandtsen

Hi,  Is it possible to draw a heatmap with plotPlaid from some (or all) chromosomes together? How? &nbsp

diffhic GRanges

updated 10.1 years ago • rulicosentino

<div class="preformatted">Hi, I am encountering an error when attempting to retrieve data from the X chromosome using GViz. The error is unclear to me and I would greatly appreciate some help. The code and error and sessionInfo() are below. Please note that I have tried the code with and without ucscChromosomeNames=FALSE. Thank you very much. best wishes, Chris CODE: ################…

biomaRt Gviz biomaRt Gviz

updated 12.7 years ago • Christopher T Gregg

is mainly CO92 (3885 ORFs) but has 944 ORFS from KIM not found in CO92 (and some genes are on main chromosome, and some on virulence plasmids). The GAL file does not contain any genbank IDs. It does contain locus names. The gpr...not sure if all features in the chip are present in the genbank files. If I wanted to use the KIM chromosome as the reference, however, the genes from CO92 would not …

Microarray geneplotter limma AnnBuilder genomes Microarray geneplotter limma AnnBuilder

updated 20.7 years ago • Palmer, Lance

<div class="preformatted">This is an automated message sent out weekly to report recent changes to Bioconductor packages. Please see the URL http://www.bioconductor.org/changelog.html for a complete history of changes. Unless otherwise noted, these changes apply to the developmental packages only. ---------------------------------------------------------------------- - Oct. 31 2003: metaD…

Annotation GO Biobase Annotation GO Biobase

updated 22.1 years ago • madman@jimmy.harvard.edu

<div class="preformatted">Hi all, I'm constructing a bunch of GFF files to load into a genome browser to display CHiP-on-chip data, and for this I need the length (in bases) of specific mouse chromosomes. I was hoping biomaRt might be able to do this, and I see an attempt was made here ( http://tinyurl.com/y7rbzo) which I...browser to display CHiP-on-chip data, and for this I need the len…

biomaRt biomaRt

updated 19.1 years ago • Shamit Soneji

<div class="preformatted">Hi£¬ according to the readme file, there are someting wrong in the bsmooth-align-0.8.1 install. the detail in the following: g++ -DUSE_PTHREADS -DMERMAN_VERSION="\"0.4.1-beta1\"" -lpthread -Wall -g -DNDEBUG -O3 -o merman mer_index.cpp alphabet.cpp check.cpp merman.cpp qual.cpp read.cpp seeds.cpp edit.cpp hit_set.cpp refmap.cpp annot.cpp threading.cpp color_dec.cp…

updated 12.0 years ago • liwei_epi

Hello List, I am trying to graph the position of probes ~50 nucleotides in length along a chromosome and am looking for the best way to accomplish this. So far I have tried the genomeGraphs package and can plot a chromosome

graph GenomeGraphs ASSIGN graph GenomeGraphs ASSIGN

updated 14.5 years ago • Pete Shepard

preformatted"> Dear Biocore Team, I'm using cPlot()/cColor() from package annotate to produce chromosome plots and am very impressed how easily this can be achieved. However, unfortunately, the chromosomes are plotted

annotate annotate

updated 16.4 years ago • Axel Klenk

Package that could help me simply draw something like this by using gene locations and numeric copy number values and it doesn't need a complicated class of data as input? <img alt="" src="http://www.bloodjournal.org/content

copynumber alteration

updated 7.2 years ago • Arman Shahrisa

values yy <- unique(y) o <- order(yy) yi <- match(y, yy[o]) ## draw 'chromosomes' with(chrs, { idx <- match(yy, Chromosome) panel.segments(1, seq_along(yy), Length[idx][o], seq_along(yy)) }) ## plot genes panel.segments...structures needed to use my functions genes <- data.frame(Id=rep(id, sa…

Annotation Cancer geneplotter idiogram rtracklayer Annotation Cancer geneplotter idiogram

updated 16.6 years ago • Martin Morgan

class="preformatted">Are there any packages available for making a karyogram with ideograms of each chromosome? I have looked at GenomeGraphs, Idiogram and a number of other packages but they seem like they have been designed...to draw a single chromosome at a time. Ideally, I would like to produce pictures similar to those obtained from karyoview with a bit more programmatic...control. I …

idiogram GenomeGraphs idiogram GenomeGraphs

updated 17.5 years ago • Michael Gormley

Hi, I'm wanting to plot some alignments from Barley (Hordeum vulgare) which has 6 chromosomes beyond the limit of .bai index files (2^29). Are there any plans to enable .csi index files or is this a difficult ask...Currently the only real option is splitting chromosomes pre-alignment. Thanks, Steve

gviz

updated 9.0 years ago • Steve Pederson

Dear all, I'm trying to plot a certain number of SNPs and have in the x-axis both, the chromosomal position and their labels. I have imported the SNP information from...Mb") fixed(SNP_location) <- TRUE SNP_location</pre> This code returns a plot with the chromosomal positions in the x-axis and the SNPs in their correct location: <img alt="" src="http://i.imgur.com/qJonMkf.jp…

ggbio ggplot2 genomics plot

updated 9.3 years ago • oswaldo.lorenzo

Wondering how I can go about outputting the following command which would have the chromosome map already applied? So for instance instead of "chromosome \# 26" representing the X, it is already changed in the binding

diffbind chipseq differential binding analysis

updated 8.1 years ago • rbronste

research paper (Plant Physiology 2008, vol 148, pp. 1189-1200). That test is about the occurrence number of a kind of gene in separate chromosomes. For instance: The observed gene number in chromosome A is 36. The expected gene...number in chromosome A is 30. Then, the authors got a probability 0.137 by distribution test on this trial. In this test, a Poisson

updated 16.4 years ago • Mao Jianfeng

div class="preformatted">Hello, I am trying to analyse data from a single chromosome e.g. chromosome 3 obtained from array CGH using the aCGH library within bioconductor, however I get the following...error message : >hmm(ex.acgh)<-find.hmm.states(ex.acgh, delta=1.5) sample is 1 Chromosomes: 1 Error in kmeans(y, 2) : subscript out of bounds Error in array(x, c(length(x), 1…

aCGH CGH aCGH aCGH CGH aCGH

updated 18.8 years ago • Ruppert Valentino

So I output a matrix from DiffBind as my input into DESeq2, with the chromosome positions being removed from the count matrix, just leaving the first column key as a reference followed by the...wondering how I can remap this list to the original matrix output from DiffBind so I can recover the chromosome positions since this contains only the key.  Thanks! &nbsp

deseq2 deseq diffbind differential binding analysis

updated 8.0 years ago • rbronste

Hi, By any chance, do anyone have any recommendations which software could provide me with chromosome bins from a denovo contig assembly by using HiC data and without any annotation? Thank you in advance

diffhic gothic hicup hic-c hic

updated 7.1 years ago • mictadlo

your suggestions and with one additional step it works perfectly now. Apart from setting the chromosome identifier in the ranges from 2 to chr2, the active chromosome for the bmTrack also needs to be set to chr2 after...BiomartGeneRegionTrack(start=st, end=ed, > chromosome="chrX", > genome="hg19",showId = > …

Annotation ideogram Gviz Annotation ideogram Gviz

updated 12.4 years ago • Martin Rijlaarsdam

for the PureCN.R --maxhomozygousloss option is 0.05,1e+07.  Does this mean that if entire chromosome arms are lost, they must not total more than 5% of the genome?   &nbsp

Purecn maxhomozygousloss

updated 7.1 years ago • twtoal

on a steep learning curve with R & am trying to convert a large batch of mouse entrezIDs to homologous human entrezID & when sending as a batch to biomaRt the search result doesn't contain the query string (is this...only be human or mouse # Warnings will need to be suppressed in the case of no match existing homologs <- c() no.homolog <- c() if (…

convert biomaRt convert biomaRt

updated 18.7 years ago • Steve Pederson

div class="preformatted">Hello list Is there a way to plot chromosome band names along an ideogram using genome graphs. I realize that this can be done in quantsmooth but I prefer the

ideogram quantsmooth GenomeGraphs ideogram quantsmooth GenomeGraphs

updated 14.5 years ago • Pete Shepard

div class="preformatted">Hi I have a liste of reads that map to the genome in certain position (chromosome | position) and i would like to know which function allows that. Thanks in advance for your help, Regards, Ramzi [[alternative

updated 16.1 years ago • Ramzi TEMANNI

Hello, I'm trying to plot genomics data in the vicinity of the Tlr7/8 genes on the X chromosome using karyoploteR and there seems to be an issue with the coordinates in that region: ``` region <- toGRanges("chrX...seqinfo(TxDb.Mmusculus.UCSC.mm10.knownGene) ``` shows a seqlength of 171031299 for chrX so the chromosome end should be roughtly 3.6Mb away from my ROI. I was thus wonderi…

TxDb.Mmusculus.UCSC.mm10.ensGene TxDb karyoploteR

updated 13 months ago • remi-xavier.coux

July 30, 2003 - Metadata: a new annotation data package -homology was added to the link to metadata. The package containes data for pairwise best matches for different organisms...JZ July 25, 2003 - AnnBuilder: a new function homoPkgBuilder was added to build a homology data package using the homology data provided by NCBI. JZ</div

Annotation Annotation

updated 22.4 years ago • madman@jimmy.harvard.edu

Dear all,        We are using Diffbind to examine differential peak enrichment between male and female samples. Our input control is from the same sample before the immunoprecipitation stage. We have 4 replicates per treatment. The way we are using the Diffbind commands is exactly like given in the vignette and the manual. It is our understa…

diffbind

updated 9.9 years ago • surjray

I am facing some problems when using the command readBPM(). The readBPM() function doesn't return chromosome and position that are needed for DNAcopy's CNA function. Can someone help me? How and where could I get and extract...the chromosome and position using readBPM() function? Thank you. regards, jingxian</pre

limma #illuminaio #DNAcopy #readBPM #idat

updated 11.2 years ago • jingapril41

ontology terms on the graphic output because the names run off the screen. Also, when I plot a pie chart of GO terms at a high level, there are too many GO terms on the pie chart and I can't read them. regards Anthony -- ______________________________________________

GO GO

updated 20.9 years ago • Anthony Bosco