object with 4068 ranges and 6 metadata columns:
seqnames ranges strand | name score signalValue
<Rle> <IRanges> <Rle> | <character> <numeric> <numeric>
[1] chr22 [16554493, 16554606...chr22 [17325983, 17326150] * | Rank_84671 …
Order by: Relevance
to join Affymetrix U133A and
B
arrays. The rownames of the expression matrix are set to the probe
names. To do this I want to treat all the probe names that are shared
between the arrays as unique by appending an "_A" or "_B". I do this...by
finding the names of the probe that are shared and then running:
rownames(expr.matrix[match(ProbeIntersect,rownames(expr.matrix)),]) <..._A",sep=""…
TRUE, single.end=FALSE, param=param)
Error in array(x, c(length(x), 1L), if (!is.null(names(x))) list(names(x), :
'data' must be of a vector type, was 'NULL'</pre>
Could someone explain me the error?
Does the error come from my reads...Object)
24: initialize(value, ...)
23: initialize(value, ...)
22: new("SummarizedExperiment0", NAMES = names, elementMetadata = rowData,
…
updated 10.1 years ago • user31888
modules_names, col = module2colors_colors)
)
cell_type_legend <- Legend(
labels = names(celltype2colors), # Cell type names
legend_gp = gpar(fill = celltype2colors), # Corresponding colors
title = "Cell Type"
)
cell_subtype_legend...lt;- Legend(
labels = names(cellsubtype2colors), # Cell subtype names
legend_gp = gpar(fill = cellsubtype2colors), # Corresponding c…
updated 14 months ago • nromerov
read count. after I get them, how can I reach to the gene I want? because it wont give me the every name of the gene, right?
would be great if you can help me
updated 2.1 years ago • Gülsüm
p.val < 0.1, 1:5]
listPathway=rownames(output.bidir)
geneSet<-vector(mode = "character",length = length(listPathway))
for (j in 1:length(listPathway)){
termselec=listPathway[j]
gs=unique(unlist
updated 8.6 years ago • aurelie.nicolas
treatments, I have created a heatmap with the geneIDs but I am struggling to find a way to add gene names or alternatively produce a list of gene names that are deferentially expressed. I have a GFF3 file and a cds file for the
updated 2.9 years ago • Chelsea
I have a huge list of gene names, and I'd like to map corresponding gene IDs to each name. I've tried using this R library: `` org.Hs.eg.db ``, but it creates...more IDs than names, making it hard to map the results together, especially if the list is long.
Example of an input file (7 gene names):
RPS6KB2...read input file
GeneCol = as.character(input$Gene.name) #a…
updated 7.5 years ago • Bayram Sarilmaz
I get the error:
Computing DABG calls... Error in 0:max(counts) : result would be too
long a
vector
In addition: Warning message:
In max(counts) : no non-missing arguments to max; returning -Inf
Using the human data in the...GeneFeatureSet (storageMode: lockedEnvironment)
assayData: 1102500 features, 33 samples
element names: exprs
protocolData
rowNames: TisMap_Brain_01_v1_WTGene1.CEL
TisMa…
updated 12.0 years ago • Peter Crisp
I used the `` AnnotationDbi::mapIds `` function over the `` EnsDb.Mmusculus.v79 `` package to map Ensembl Gene IDs back to entrez id over a a long vector of ENSG Ids.
I expected this to return a 1:1 mapping when `` mapIds(..., multiVals='first') ``, but was surprised that this returned several entrez ids concatenated with ";" for a given ensembl gene id, for instance:
<pre>
R&am…
updated 8.6 years ago • Steve Lianoglou
chr, ll, unique)
Error in unique.default(X[[as.integer(1)]], ...) :
unique() applies only to vectors
>ll.chr <- tapply(unlist(chr), ll, unique)
Error in tapply(unlist(chr), ll, unique) :
arguments must have same length
>length
updated 21.5 years ago • Irene Li
mildly updated; new HTML vignette on working with the ontology
- EMBL-EBI recased all field names to upper case; code using field names must be modified
updated 10.4 years ago • Vincent J. Carey, Jr.
I've been trying to get the qvalue package to work for me. However, when I put in a vector of p-values I get the following error:
<span style="background-color:Yellow">`` Error in smooth.spline(lambda, pi0, df = smooth.df...are not allowed ``</span>
I have tried inputting the p-values in various ways.
Consider a vector of p-values such as `` .0009, .02, .423, .012, .003 `…
updated 7.9 years ago • ilikescience1
version number for a particular BioC version.
I know all\_group() will return the list of package names, but I also need the versions. Where can I get these from?
Cheers,
Nathan
updated 9.8 years ago • nathan.watsonhaigh
<div class="preformatted">Dear group,
I have 2 questions to ask:
Question 1:
Give a pathway name for KEGG, how do I get all the
genes involved in that pathway.
>library(KEGG)
>wnt <- get("04310", KEGGPATHID2NAME)
now how do I get gene names in wnt pathway. Here I am
not interested in taking say HGU133a chip and map all
probeset ids to wnt. I just need genes in wnt.…
header. Constructor of `new('GraphTrackLine', ...)` object requires color argument of type `integer` (vector). I have provided argument value `color=col2rgb("red")[,1]` and results output track header formatted as
track name=
<name> description...letter ',"255","0"'
Please help me to workaround color property format incompatibility.</desc></name
updated 6.8 years ago • tanas80
of two types, one or more vignettes and a reference manual; and they
have the same file name, PackageName.pdf. When downloaded some file
name manipulation is required, or accept PackageName(1).pdf.
I suggest the...documents be given different names, for example the
reference manual could be named PackageNameRefMan.pdf. Package
checking could enforce the rule.
-- output
updated 11.4 years ago • Guest User
s no useful info to
extract
> > what I want
>
> This is NOT two ids per row. It is one vector. R outputs two
> elements per row only because your screen is wide enough for that.
>
> If you do:
>
> tmp <- as.character...1:4340867] 28 29 29 28 29 28
29 28 27
> >> > 29
> >> &g…
Hi,
Is there an option to keep the original file name when adding a 'web' file by `bfcadd`?
For example,
```
bfc0 <- BiocFileCache(tempdir(), ask = F)
add1 <- bfcadd(bfc0, "bwa",
fpath = "https://raw.githubusercontent.com...tl_bwa.R"))
add1
## "/tmp/RtmpzSEpeG/b01175a39e7e_tl_bwa.R"
```
A prefix was added to the file name. Is it possible to keep the ori…
updated 5.8 years ago • Qiang
the -log10 of the FDR value and multiplies it by the sign of the log fold change. Then I order the vector from decreasing to increasing values so the downregulated genes are at the top while the upregulated genes are at...in the code below:
```r
newRank_pvalueAndFC = -log10(myDEresults$FDR) * sign(myDEresults$logFC)
names(newRank_pvalueAndFC) = rownames(myDEresults)
newRank_pvalueAndFC = …
updated 20 months ago • sropri
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", but 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 annotation. Bu…
updated 13.3 years ago • sun
with 10 cases and 7 controls:
[1] 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0
you can direct this line to a vector with vectro.cl <-rep(c(1,0),
c(10,7)).
But i would still like to knoe how to generate the .gnames file, wh?re
all the
gene names are
updated 20.2 years ago • Assa Yeroslaviz
Dear All,
Using tximport for salmon, I noticed that when the name of transcripts are like this:
ENST00000335137.3|ENSG00000186092.4|OTTHUMG00000001094.1|OTTHUMT00000003223.1...OR4F5-001|OR4F5|918|CDS:1-918|
It cannot read and returns an empty vector but does not give an error!!. I replaced "." with "|" and it worked fine for me on line 296:
if (ignoreTxVersion) {
&n…
in `collect()`:
! Failed to collect lazy table.
Caused by error in `db_collect()`:
! Arguments in `...` must be used.
Problematic argument:
..1 = Inf
Did you misspell an argument name?
Run `rlang::last_trace()` to see where the error occurred
updated 23 months ago • goldenboy
in `collect()`:
! Failed to collect lazy table.
Caused by error in `db_collect()`:
! Arguments in `...` must be used.
x Problematic argument:
. ..1 = Inf
i Did you misspell an argument name
The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1. Please report this to the mailing list.</pre>
I checked online but none of the offered solutions...1' count = '0' datasetConfigVersion = '0.6' header='1' requestid= 'biomaRt'> <Dataset name = 'hsapiens_gene_ensembl'><Attribute name = 'ensembl_transcri…
nbsp; <character> <character> <numeric> <numeric>
ENSG00000180155...nbsp; &…
updated 9.9 years ago • gmerino
expression values with SYMBOL...
<strong>Error in array(x, c(length(x), 1L), if (!is.null(names(x))) list(names(x), : </strong>
<strong> 'data' must be of a vector type, was 'NULL'</strong>
> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform
updated 11.1 years ago • mali salmon
<div class="preformatted">
Hi all,
I must admit that I am quite new to both methylation data analysis and
R. I am currently analyzing IlluminaHumanMethylation450k array. Before
using BMIQ method I have used lumi package to perform a background
correction and created a MethyLumiM object. Is it possible to use
MethyLumiM object as input in BMIQ method? When I try to use it, I got
following e…
but I got an error report
Error in stop_if_wrong_length("'seqnames'", ans_len) :
'seqnames' must have the length of the object to construct (1) or length 1
here is my code
library(BayesPeak)
rm(list=ls())
options(stringsAsFactors
updated 3.8 years ago • 建国
Hi everyone,
I'm trying to use CHIPseeker for CutnTag data, and had a question regarding getting the names of each annotation. I've used annotatePeak to get an idea about the promoter, exon and intergenic region, but is there a...everyone,
I'm trying to use CHIPseeker for CutnTag data, and had a question regarding getting the names of each annotation. I've used annotatePeak to get an idea a…
updated 4.6 years ago • rithika.behera
res <- nbinomTest( cds, "N", "T" )
I get numbers under ids because on page 4 we removed the gene names.
countsTable <- countsTable[ , -1 ]
How can i get my res to match what is in the manual with gene names
under id?
Thanks,
Mary Ann
lt;- getBackSplicedJunctions(gtf)
Error: Can't combine `..1$id`
<logical> and `..2$id` <character>.
Run `rlang::last_error()` to see where the error occurred.
I ran `rlang::last_error()` but couldn't make any sense of it
>...error vctrs_error_incompatible_type="">
Can't combine `..1$id` <logical> and `..2$id` <character>.
Backtrace:
…
updated 5.2 years ago • Terra
for your help,
Kathi
> findOverlaps(ensembl.genes,exons)
Error in genome(y) :
no slot of name "genome" for this object of class "Seqinfo"
> head(exons)
GRanges with 6 ranges and 7 elementMetadata values:
seqnames ranges...strand | phase section.id
<rle> <iranges> <rle> | <numeric> <character>
[1] chr1 [ 704549, 7…
updated 14.2 years ago • Kathi Zarnack
readAligned(dir,âs_1_sequence.mapâ,âMAQMapâ)
Using this, I get an error that âpatternâ must be
âcharacter(1)â. Alternately, I define pattern by:
pattern <- âs_1_sequence.mapâ
aln <- readAligned(dir,pattern,âMAQMapâ
updated 16.4 years ago • Jessica Hunter
Could you add selected row names to a ```pheatmap``` instead of including them all using ```show_rownames = T```?
Something similar was asked few years ago here https...10, show_colnames = F, show_rownames = labgenes, color = colorRampPalette(rev(brewer.pal(n = 7, name ="RdYlBu")))(100
nbsp;contains more information than the species and genus, that will not be used in the package name. For example, I create a TxDb object:
<pre>
url <- "http://plasmodb.org/common/downloads/Current_Release/PbergheiANKA/gff...Genetics, TxDb, Plasmodium_berghei_ANKA
</pre>
So, is there a way to make the package name be `` TxDb.PbergheiANKA `` when creating it with `` makeTxDb…
updated 10.6 years ago • Diego Diez
api/search/downloads/alternative...
formatting gwaswloc instance...
NOTE: input data had non-ASCII characters replaced by '*'.
Error in `[[<-`(`*tmp*`, name, value = numeric(0)) :
0 elements in value to replace 24454 elements
> gwascat <- makeCurrentGwascat...gwas/api/search/downloads/alternative...
formatting gwaswloc instance...
Error in `[[<-`(`*tmp*`, na…
updated 9.8 years ago • enricoferrero
the export method in rtracklayer for the GRanges class
requires that the GRanges object have unique names. The error message
given when names are not unique is the following:
Error in export(object, FileForFormat(con), ...) :
cannot...export object of class 'GRanges'
As one can easily make a case that non-unique names may be
troublesome,
I am curious to know whether you intentionally disall…
updated 13.0 years ago • Samuel Younkin
I am having trouble getting specific coefficient names after running DESeq2. The coefficients I get when I run resultsNames(dds) are "Treat1", "Treat2", etc instead of "Treat_B_vs_A
updated 4.7 years ago • jkhudyakov
div class="preformatted">Hi,
I was trying to map gene symbols to gene names using the org.Hs.eg.db
package. I first convert the gene symbol to an entrez id, and then
convert that to a gene name (example...code below). However, during this
process I can't get the gene names for some of the genes:
--------------------------
library(org.Hs.eg.db)
### First two genes are ok...
symbols <…
<div class="preformatted">Hi,
I'm creating my limma design matrices by hand and am just wondering
whether the sample names in the matrix actually matter or whether they
may be arbitrary as long as they reflect the ascending order of array
columns...Hi,
I'm creating my limma design matrices by hand and am just wondering
whether the sample names in the matrix actually matter or whether they…
div class="preformatted">Dear all,
I have a script that generates a large number of gene sets (vectors of
gene names) and would like to apply a functional analysis (e.g. how
many transcription factors occur in each gene...set? how many kinases...
etc.). I can convert the gene names into different formats using
biomaRt, however, the only functional analysis tools I have found in R
apply an enr…
updated 15.8 years ago • Rainer Tischler
appreciated.
#KEGG Pathway Analysis
```{r}
#place ENSEMBL into ENTREZ id format
ids<-bitr(names(original_gene_list), fromType = "ENSEMBL", toType = "ENTREZID", OrgDb=organism)
dedup_ids = ids[!duplicated(ids[c("ENSEMBL")]),]
df2...g[g$gene_id %in% dedup_ids$ENSEMBL,]
df2$Y = dedup_ids$ENTREZID
# Create a vector of the gene unuiverse
kegg_gene_list <- df2$log2FoldChange
```
```{r…
updated 4.3 years ago • ICELANDICWATER
<div class="preformatted">
Hi I'm trying to read in cel file names from Affy MoGene-2_0-st
arrays, however I am receiving error message indicating that my cel
file names are not of the character class when it appears that they
are. My phenodata is read in successfully.
Here is my code and error:
>celfiles = list.files(path = ".", pattern = ".CEL$", all.files =
FALSE,
full.names = F…
Hi,
Can we change the name of the ColAttributes in the image generated by dba.plotHeatmap?
As I have two attributes in my data `DBA_CONDITION`, `DBA_FACTOR...but want to name "Factors" as "Histone Mark" in the figure generated by `plot()` or `dba.plotHeatmap()`. Is it possible to do so?
Thanks
updated 6.4 years ago • researcher
sl <- as.integer(unique(sl))
So if two or more chromosomes have the same length this vector will be shorter than the `sn` vector which holds the names of the chromosomes. Although uncommon, it happens if the reference
updated 5.4 years ago • asafpr
to create a AnnotationTrack from a Grange object. However, I got this error "Error: cannot allocate vector of size **1817.1 Gb**". My grange contains 493849 rows.
gr
GRanges object with 493849 ranges and 0 metadata columns:
seqnames...sequences from an unspecified genome; no seqlengths
DNAse_Union_merged <- AnnotationTrack(gr, name="DNAse_Union_merged", col="#00FFFF"…
updated 6.5 years ago • rejpl
div class="preformatted">Dear Jay,
Actually makeContrasts() will recognize an expression or character
string, but it won't always
correctly parse a character-valued variable.
The reason is that makeContrasts() expects...to get expressions.
Although it does also allow
character strings to define the expressions, it is too difficult to
correctly distinguish
character vectors from expressions..…
no results would be filtered out but it doesn't seem to have worked that way.
geneList below is a vector of fold changes with ensembl IDs as names
```r
gsea_res <- gseGO(geneList=geneList, OrgDb=org.Hs.eg.db, keyType="ENSEMBL
updated 18 months ago • yesitsjess
showed significant differences in our previous experiments using different material. The complete name of the pathway after the analysis is "AGE-RAGE-signaling pathway in diabetic complications" (https://www.genome.jp/pathway...activate AGE-RAGE signaling) and that is why I ask myself if it is accepted to shorten the pathway name to "AGE-RAGE-signaling pathway"? On Wikipathway for example, you ca…
your code, you can do ...
library(gridGraphviz)
nodeShape <- rep("box", length(nodes(testG)))
names(nodeShape) <- nodes(testG)
rag <- agopen(testG, "",
nodeAttrs=list(shape=nodeShape))
grid.newpage()
grid.graph(rag)
# Get label...names
grobs <- grid.ls()
labelIndex <- grep("label", grobs$name)
labelPaths <- grobs$gPath[labelIndex]
for (i i…
<div class="preformatted">Dear mailing list,
I have a problem with rtraclayer that you can hopefully help me with.
I'm trying to export tracks to the UCSC browser or to BED files
through
rtracklayer, but I have problems with the blockStarts and blockSizes
fields
functioning, and get a
>export(targetTrack, format="bed", con="bed.bed")
Error in df[[2]] + lastSize : non-numeric argume…
updated 15.2 years ago • Johannes Waage
to both 1to5kb and introns of the same gene.
Could you help me about this? Thanks.
This is R code named "test.R" I was using:
input = "test.txt"
library(annotatr)
#annots =c('mm10_cpg_islands', 'mm10_cpg_shores', 'mm10_cpg_shelves...build_annotations(genome = 'mm10', annotations = annots)
extraCols = c(diff_meth = 'character', mu0 = 'character', mu1 = 'cha…
updated 7.9 years ago • xie186
<div class="preformatted">hi again everybody,
the original post was not published at the list, so this is just to
confirm that the fix that you kindly provide has been included in the
updated development (1.7.5) and release (1.6.2) versions of the GSVA
package.
thanks again for bug reporting, and this time, even fixing!! :)
robert.
On 01/16/2013 11:55 AM, Luca Beltrame wrote:
> He…
updated 13.0 years ago • Robert Castelo
div class="preformatted">Hi eveyone,
my name is Priscila, and I'm beginning to use Limma package to analyse
my
microarray data.
Could someone help me? I can't even start...I
can't
read my file Targets.txt using the Limma package. I don't know which
information this file must contains, except for the .gpr file. Does
anyone
have a model?
Thanks!
Priscila
[[alternative HTML version de…
Hello,
Sorry for that very basic question: I have raw RNA-seq count data. The row names are genes, the column names are short sequences (e.g., AAACCTGCAATCTACG.1). Aren't these supposed to be sample names? What...is the name of such a file format? (Couldn't find anything online, though don't know what I have to search for.)
The ultimate goal is to have
updated 4.4 years ago • Anne
end_position insideFeature distancetoFeature
shortestDistance
<factor> <iranges> | <character> <character>
<character> <numeric> <numeric> <character>
<numeric> <numeric>
1 STPG1-2 chr1 [24736757, 24737528] | 1 -
STPG1-2 24683489...space ranges | peak
strand
&l…
updated 12.0 years ago • Julie Zhu
difficulties to use regular expressions in R.
My problem is that I can't recover in a vector the data that I want to recover.
My R script is the next:
<pre>
variable<-file("BestFitnessSBML_L1V2_exported.xml...r")
while (length(line <- readLines(variable, n = 1))) {
results<-grep('.*<parameter name=\"a1\" value=\"0.1…
updated 10.5 years ago • fabien.chambodut
Greetings! I am new to this forum and posted a question recently to the RStudio community. A kind soul, Mara Averick pointed me to this forum.
My objective is to annotate a table of gene expression data "say for organism A" with information on orthologues from "organism B", as an additional column on a table. I watched tutorials online (YouTube) on how do do this using the BioMart GUI. Many clic…
updated 7.2 years ago • lm795
Recent ...
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