<div class="preformatted">Hi all,
I'm just wondering if there would be a direct way to convert an
IRanges to an Rle, as in: as(rng,"Rle"). At the moment, I can convert
my IRanges into an integer vector and cast that as an Rle
(Rle(as.integer(rng)), but that is not extremely efficient on a long
IRangesList (with > 700,000 IRanges...an
IRanges to an Rle, as in: as(rng,"Rle"). At the m…
Order by: Relevance
tumor, control). This is necessary if you
want to produce a DESeq output. The conditions should be a named
vector, the names being the actual filenames: e.g. in your case
conditions=c("TTGR1.bam"="tumor"). Asking for a DESeq output...easyRNASeq package to obtain read counts so
that I can proceed with my analysis for DESeq. However I must be doing
something wrong in giving it the right arguments, …
updated 13.5 years ago • delhomme@embl.de
exon + condition:exon, flattenedfile=flattenedFile)
Error in strsplit(rownames(dcounts), ":") : non-character argument</pre>
Here is what countFiles and sampleTable look like:
<pre>
> countFiles
[1] "/Volumes/TOSHIBAEXT/3.mapping
updated 9.7 years ago • sakura.nussbaum
of interest)
4) Calculate the ratio of average expression for each gene and export this as a named and sorted numeric vector (which serves as the gene list for clusterprofiler functions. This vector contains all...NULL,
samp_id1 = "d12ko",samp_id2 = NULL)
all<- enricher(names(f480_d12_KOvsWT_list),
TERM2GENE = msig_HAL…
updated 7.5 years ago • atakanekiz
Hi BioC List from {sunny}San Diego, CA!
[Question]:
* How do you map KEGG gene IDs to textual gene names, gene
descriptions
via BioC?
For example, I am interested in knowing which genes are
involved in the calcium signaling...pathway in rattus norvegicus,
so I did:
> library(KEGG)
> # map pathway id to pathway name
> KEGGPATHID2NAME$"04020"
[1] "Calcium signaling pathwa…
updated 18.0 years ago • Elliot Kleiman
I have used GCDquery() (from library "TCGAbiolinks" ) for months now with no problems, but now the following:
`` library("TCGAbiolinks") ``
`` PreClin<-GDCquery(project="TCGA-BRCA",data.category = "Clinical",barcode = Breast_Tumor_barcodes) ``
returns the following error:
<code>> source('~/.active-rstudio-document')<br/>
--------------------------------------<br/…
updated 8.2 years ago • jrlarsen
TRUE
bf <- Rsamtools::BamFile(file, index = index, asMates = pairedEnd)
# Rename chromosome names from UCSD to non-UCSC
GenomeInfoDb::seqlevels(selection) <- sub(
"chr",
"",
GenomeInfoDb::seqlevels(selection))
param <- Rsamtools...scanBamFlag(isUnmappedQuery = FALSE))
reads <- if (as.character(seqnames(selection)[1]) %in% names(Rsamtools::…
updated 9.1 years ago • stianlagstad
Hi,
I am trying to convert a list of KEGG pathway name to corresponding KEGG IDs.
To do that, I am using KEGG.db, Version 3.1.2. It seems that this package is not complete, for example...nbsp; keggid2name\["04261"\]
Do you have any idea about where can I find complete list of pathway names and IDs
I am working with a custom Affymetrix array. I am now looking for a
way to access the probe names, that is the probe set name plus an
identifier. I have understood that this would be what would be the
atom number in the
<div class="preformatted">dear list,
i would like to produce a GO graph where the labels of the nodes are
formed by the GO identifier and the GO term and these two pieces of
information appear in two different lines within the node, in order to
draw nodes somewhat narrower than if i have these two pieces in one
single line.
the following code does the job putting GO ID and GO term in the …
lt;Rle> <IRanges> <Rle> | <integer> <character> <integer> <character>
ENSMUST00000000001.4 chr3 [108109403, 108109421] - | 57602 ENSMUSE00000404895.1...transcripts. I tried the more generic `` getSeqs ``, but it inserts transcript ids into the text and names r…
updated 9.9 years ago • Jake
<div class="preformatted">Hello,
I tried to draw the gene model by using autoplot() in ggbio package
with
the following codes.
library(ggbio)
library("TxDb.Hsapiens.UCSC.hg19.knownGene")
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
data(genesymbol, package = "biovizBase")
autoplot(txdb,which = genesymbol["ACSS2"],names.expr ="tx_name")
There is only one straight line and no any exo…
affy") || stop("cannot load applera without affy")
setClass("applera", representation(Organism="character",
Geneid="character", Signal="exprSet", Sdev="exprSet", Cv="exprSet",
Sn="exprSet", Flags="exprSet", Ctrl="list"), contains="exprSet...geneid", signature(object="applera"), function(object) {
primaryId <- as.vector(object at Geneid)
names(primaryId) <- geneNames(object at Signal…
Noticed a discrepancy in config file parameter names.
In all documentation, the DBA$config$edgeR$bTagwise and DBA$config$DESeq2$fitType parameters are structured as written...error:
"Analyze error: Error in pv$config$DESeq2$fitType: $ operator is invalid for atomic vectors"
I think this may only occur if the values are explicitly set in an external config, and a workaround seems to be t…
<div class="preformatted">Hi,
i need some helpediting my resluts.
I have a data frame( matrix ), whereas on the first column are the
names of my
items. Then I have a second object. This is the output of the line:
> list.siggenes(data.out, delta)
"item_1! "item_2" "item_3...some helpediting my resluts.
I have a data frame( matrix ), whereas on the first column are the
names of my
i…
updated 20.2 years ago • Assa Yeroslaviz
<div class="preformatted">Hi,
I've just realized that a call to unique on a DNAStringSet would
result in the names slot to disappear. There's nothing about this in
the documentation, but if that's the desired effect, warning about it
would...preformatted">Hi,
I've just realized that a call to unique on a DNAStringSet would
result in the names slot to disappear. There's nothing about th…
updated 13.4 years ago • Nicolas Delhomme
Dear Dr. Leek,
I am a new user of the SVA package and try to remove the batch effects for our data. Your sample data works well. When I start my own .csv data (name as HBVHCC), the following code showed the errors. Is the code useful for the .csv file? Do you have a code to solve this problem? I appreciate your support.
Best Regards,
Jing Shen
mod = model.matrix(~as.factor(cancer)…
updated 9.6 years ago • js2182
error when plotting the heatmap:
`` Error in cutree(tree, cutree_n) : elements of 'k' must be between 1 and 3 ``.
I cannot figure out what k is (I thought the number of cluster to be formed, but why does this need to
pre>
It turned out that I am able to use the function with multiple reference sequence names like this, for example:
<pre>
bamDataRanges <- getReadCountsFromBAM(BAMFiles,
sampleNames=paste("Sample",1:2),
<strong>refSeqName...quoted below) suggests that the function is only capable of handing a s…
updated 8.9 years ago • Mohammad Alkhamis
and calling grep on the term summary:
grep("chromosome", Term(x))
Since Term(x) returns a character vector of length one, if a match is
found the return value of grep will be 1. If no match is found it
will be integer(0) (a...zero-length integer vector).
If x (the GOTerms instance) was a list, then we would have either x[1]
or x[integer(0)]. But since x is an S4 class with no "[" method
by
default, or accept an array of filenames. My filenames are the barcode
of the LDA, not the sample name.
In readCtData is there a way to assign sample = from a column within
the
data files?
Regards,
RH
</div
lcpm<-cpm(y, log=T)
head(lcpm)</pre>
gives first row with unique numeric ID which denotes gene names from data file. How to export name of genes into \*.csv file but with name of genes ?
<pre>
write.csv(highly_variable_lcpm, row.names
updated 7.7 years ago • Björn
div class="preformatted">An embedded and charset-unspecified text was scrubbed...
Name: not available
Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20080407/
e5a2c438/attachment.pl</div
updated 17.7 years ago • Keyel, Peter
div class="preformatted">An embedded and charset-unspecified text was scrubbed...
Name: not available
Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20070625/
b5639236/attachment.pl</div
updated 18.5 years ago • James Anderson
div class="preformatted">Hi BioC,
How can I access gene names from KEEG Gene ID ?
for example : KEGG Gene ID : mmu:11479
Thank you in advance,
Saurin</div
updated 20.9 years ago • SAURIN
div class="preformatted">An embedded and charset-unspecified text was scrubbed...
Name: not available
Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20071026/
7cd3df77/attachment.pl</div
updated 18.2 years ago • Stacey Burrows
Hi,
I need to rename the DNA sequences of a phyloseq object with ASV1,2,3 and then attach the taxonomy to each new ASV name, so I could export the renamed sequences as a fasta file.
I did this successfully with a phyloseq object of PacBio sequences generated from DADA2 in R, however, when I used the same code with a phyloseq object of MiSeq sequences generated from exported files from Qiime2, it…
updated 3.8 years ago • Eman
I am reading cel files using affy::readAffy functions. To that purpose, I used a named vector files_URLs (having used GEOquery to retrieve sample information), whose values are full names of the files, and...names are the rownames I want to be used for my exprs and phenoData object (using argument sampleNames=names(files_URL)).
Operation...is correctly performed (adequate files are read, with …
updated 5.0 years ago • bastien_chassagnol
table is made by topTable, where top-ranked genes are extracted from the model. The vector back_genes has background gene PROBEIDs. DE_genes is a table with deferentially expressed genes.*
gene_IDs <- rownames...lt;- in_selection[in_universe]
all_genes <- factor(as.integer(in_selection[in_universe]))
names(all_genes) <- gene_IDs[in_universe]
lib…
updated 5.5 years ago • June.
this and it works:
ord <- function (ddir, namen){ #ddir is the directory of interest and
namen
a vector with names e.g. "GSM1008569" "GSM1008578" "GSM1008583"
open.list <- sapply (namen, function (x) {feile <- list.files (ddir,
pattern...feile$V1,
ranges= IRanges (start=feile$V2, end=feile$V3), edensity=feile$V5,
epeak=feile$V10)
}
…
org.Sc.sgdGO)
setOntology(ont='MF')
getGeneSim(as.character(labels),similarityTerm='Resnik')
My vector named labels, contain gene names such as: YAL003W YAL004W
YAL005C
YAL008W YAL010C YAL011W YAL016W YAL018C.
The result
NA
strand aggregate_gene_id..CUFF.168931.
transcripts..CUFF.168931.1.
<factor> <character> <character>
1 - exonic_section_number "001" NA
2 - aggregate_gene_id "CUFF.168931" is_full_exon "True"
3 - exonic_section_number...ranges strand | type source
> phase
> <rle> <…
updated 14.6 years ago • Kathi Zarnack
Error in DESeqDataSet(se, design = design, ignoreRank) :
all variables in design formula must be columns in colData</span>
I don't get error at all, as far as I know, all variables in the design formula (condition here) ARE
updated 9.7 years ago • wannes.nauwynck
What I currently have are all the NM\_\#\#\#\# and NR\_\#\#\#\# for the genes, but I need the gene names. I was able to get a .csv that had quite a few, so I just used R to search (grep) and match the names for me, but the file does not have...I'm hoping there is a function that allows me to input, for example, NM\_001001130, and the gene name Zfp85 would be returned.
Thank you in advance for yo…
updated 10.7 years ago • n_bormann1
nbsp; comb\_apply(countOverlaps,grlA,grlB)
Error in as.vector(x, mode = "character") :
no method for coercing this S4 class to a vector
What am I doing wrong?
Thank you for help/suggestions
updated 10.2 years ago • francesca casalino
c("chr1", "chr1"),
c(20L, 10L),
c("11M", "11M"),
strand(c("*", "*")),
names=c("read_A", "read_B")
)
x <- GRanges("chr1", IRanges(c(12, 12), width=c(6, 20)))
mapToAlignments(x, alignments) ## Empty output
However if we...strand cigar qwidth start end width njunc
#
<rle> <rle> <…
updated 6.1 years ago • Shian Su
Hi,
I have log-scaled RNA-seq expression data from 13315 genes from 3 samples and a vector of cell-type markers, with 2553 genes corresponding to 8 cell types.
I followed the `` CellMix `` tutorial and created...expression.mat ``) using the `` ExpressionMix `` function and setting the gene and sample names using the `` featureNames `` and `` s…
updated 8.2 years ago • nrubinstein
exptData(0):
assays(1): counts
rownames(25192): A1BG A1BG-AS1 ... ZZEF1 ZZZ3
rowData metadata column names(0):
colnames(103): 169377_LYMPHO_B_accepted_hits.bam
169377_celltype1_accepted_hits.bam ...
999046_celltype_m_accepted_hits.bam...999046_celltype_n_accepted_hits.bam
colData names(2): sizeFactor celltype
> genex<-DESeq(genex)
using pre-existing size factors
estimating dispers…
and normalization"
[1] "Reading normalization parameters"
list()
Using normalization method: p
[1] "Name the output file"
[1] "hps-d4-mwg-p4-slide26-10"
[1] "Name of output device"
[1] "diagPlot.hps-d4-mwg-p4-slide26-10.png"
[1] "start layout...1] "start 1"
[1] "start 2"
Error in seq.default(0, 1, length = min(17, maxcnt)) :
Length must be non-negative number
In addition: Warning messa…
updated 20.9 years ago • Georg Otto
Hello, everyone :)
I'm trying to run the ChAMP SVD analysis, however I got an error which I don't fully understand.
Anyone who does and knows how to solve?
First time I wrote down basic code
```r
champ.svd()
[===========================]
[<<<<< ChAMP.SVD START >>>>>]
-----------------------------
champ.SVD Res…
Hi,
I am using DeepBlueR trying to get several tracks from the CEEHRC project's epigenomics data (signal value) for a single gene (GJA1). The files are in bedgraph format. I can't get the value for any bedgraph (or wig file, be it for CEEHRC or Roadmap Epigenomics). However I can get the peak data (bed files). Did I missed something? I could not even find …
2.11.1 (2010-05-31)...
> library(IRanges)
> rd = RangedData(IRanges(start=c(1:10), width=2,
names=letters[1:10]), space="chr1", score=rnorm(10))
> rd
RangedData with 10 rows and 1 value column across 1 space
space ranges | score...character> <iranges> | <numeric>
a chr1 [ 1, 2] | -0.79949926
b chr1 [ 2, 3] | 1.09152227
c …
to
merge
with the corresponding rows in z1. Is this related to the precision on
auto
conversion of character to numeric? Thanks so much for your help in
advance!
r3
feature_id name chr PeakLoc peakStart peakEnd start_position...7000
6 6 6 chr2 100150 100000 100300 10000
15000 + 10000
z1
name chr peakStart peakEnd PeakLoc
[1,] "1" "chr1" "2…
strand | gene_id SYMBOL
<Rle> <IRanges> <Rle> | <character> <character>
6794 chr19 [1205798, 1228434] + | 6794 STK11
$TP53
GRanges object with 1 range and 2 metadata columns...dim: 4 118
metadata(1): header
assays(1): counts
rownames(4): GCLM TP53 STK11 SLC6A3
rowDat…
updated 8.5 years ago • Todd Creasy
Dear Florian,
I would like to show the common name of genetic elements and not the UCSC's identifier (I think it is what we see).
In addition, I would like to know if it is possible...start, to = end, trackType = "GeneRegionTrack", rstarts = "exonStarts", rends = "exonEnds",
gene = "name", symbol = "name", transcript = "name", strand = "strand", id = "name", name = "UCSC Genes",stacking="pack"…
I can filter these easily).
```r
alTrack <- AlignmentsTrack(alignment.bam, showIndels=TRUE, name="Indels")
plotTracks(alTrack,
from = 1,
to = 12000,
chromosome = "ABC")
```
Thanks already for any advice
unnecessary, just because the @cdfName slot of the
AffyBatch object didn't necessarily match the name of
the R package containing the CDF information.</div
updated 21.5 years ago • James Wettenhall
remove unnecessary pathway defintions
kegg.sets.hs = kegg.sets.hs[sigmet.idx.hs]
#creating vector of FCs with Entrez IDs as the names for the gage() function
foldchanges = res$log2FoldChange
names(foldchanges) = res$entrez...with a dataframe of the results as an input, it only produces 11 enrichment scores (the datatable named out). How can I get the datatable **out** to match the datatable…
updated 2.8 years ago • m-bihie
boxplots")
Error in as.vector(x, mode = "numeric") :
no method for coercing this S4 class to a vector
```
Thank you very much
updated 5.9 years ago • minyaaa9058
Done!
[IFNO] Estimating transcription start position...Error: subscript contains invalid names
```
Traceback:
```
Error: subscript contains invalid names
15.
stop(wmsg(...), call. = FALSE)
14.
.subscript_error("subscript contains...subset_along_ROWS(x, i, drop = drop)
7.
cov.frags[chrs]
6.
cov.frags[chrs]
5.
lapply(names(cov.frags[chrs]), function(x) { Views(subject …
updated 6.2 years ago • jason.williams
Reading ... 6Hs.243.1.gpr
> maQualityPlots(mraw)
Error in match.arg(antialias, aa.win) : 'arg' must be of length 1
> maQualityPlots(mraw,DEBUG=TRUE)
[1] "function starting"
[1] 23184 6
[1] "Re-evaluate Weight"
check Control color...and normalization"
[1] "Reading normalization parameters"
list()
Using normalization method: p
[1] "Name the output file"
[1] "6Hs.195.1"
[1] "Nam…
updated 13.4 years ago • Guest User
ht", readfile1 = reads1, readfile2 = reads2, input_format = "FASTQ", :
The number of input file names is different from the number of output file names
position goes with
what
gene a separate class (Cdf) is defined that contains a matrix with the
gene names for each entry in the probe intensity matrix. so the row
10,
column 12 entry in the Cdf matrix gives the genename for the...and columns representing chips. similarly for mm. to know what row
goes
with what gene we keep a vector with the genenames. to know what gene
is
in column, say, 10 we s…
Hi All
I have performed gometh on a 450k methylation dataset and extracted the top 20 categories using topGO. My question is, is there a way to generate a list of the gene names in the returned "DE" column, for examples the 71 genes reported in the below example?
Term  ...the top 20 categories using topGO. My question is, …
updated 8.7 years ago • r.clifford
things that I tried,
using the subset argument in boxplot, which did not work (where
cels4Plot is a vector containing the CEL file names):
ss <- boxplot(fplm,
subset = sampleNames(fplm at phenoData)== cels4Plot)
ss <- boxplot(fplm
updated 17.4 years ago • Tagett Rebecca
Do I understand it correctly, that you generate the colored
overlay from the xml as some kind of vector graphics and
merge them with the png-files of the KEGG pathways? How do
you put the EC-numbers for the proteins over them...again?
Would it be possible to have short names of the enzymes
instead?
--page 4 of the pathview vignette:
Graph from the first example above has a single layer. Node…
The codes and instructions for annotating gene names to the result table for differential gene expression analysis in DESeq2 seem to be for using Ensembl as the reference...genome in the alignment step. I'm wondering if there are instructions/codes for annotating gene names if I used UCSC hg19 as the reference genome in the alignment step? Thanks for your help
updated 10.8 years ago • anpham
Read the file with experiment design
# The file must be previously created in Excel and saved in tab
delimited format
# Columns name are very important as well as capital letters...Read Gal file gene list and verify if info is there with:
names(RG$genes)
# If answer is NULL, do the following command
####################################################################
names(RG$genes)
#10
#…
updated 14.6 years ago • Mathieu Olivier
<div class="preformatted">Hi,
I am interested in annotating lists of SNPs in R, mostly I am
interested in finding the gene a SNP is located in and for intergenic
SNPs which genes are close by. I found this code that wsa developed
with the help of Valerie Obenchain:
http://adairama.wordpress.com/2013/02/15/functionally-annotate-snps-
and-indels-in-bioconductor/
However, when I adapted this…
TxDb.Hsapiens.UCSC.hg19.knownGene, by = "gene")
unlist(exons)
# this will lost the gene name information.</pre>
How do I add the name of the gene for the exons?
I have read https://www.biostars.org/p/101513/ and 
updated 8.2 years ago • tangming2005
Recent ...
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