Displaying 20 results from an estimated 498 matches for "exon".
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exn
2012 Mar 02
3
subseting a data frame
HI,
this is my problem I want to subset this file df, using only unique
df$exon printing the line once even if df$exon appear several times:
unique(df$exon) will show me the unique exons
If I try to print only the unique exon lines
with df[unique(df$exon),] -this doesn't print only the unique ones :(
could you help?
thanks
Nat
exon size chr...
2017 Aug 25
1
splitting a dataframe in R based on multiple gene names in a specific column
...#> The following objects are masked from 'package:base':
#>
#> intersect, setdiff, setequal, union
library(purrr)
library(tidyr)
df.sample.gene<-read.table(
text="Chr Start End Ref Alt Func.refGene Gene.refGene
284 chr2 16080996 16080996 C T ncRNA_exonic GACAT3
448 chr2 113979920 113979920 C T ncRNA_exonic LINC01191,LOC100499194
465 chr2 131279347 131279347 C G ncRNA_exonic LOC440910
525 chr2 223777758 223777758 T A exonic AP1S3
626 chr3 99794575 99794575 G A exonic COL8A1
643 chr3 132601066 132601066...
2011 Jun 08
1
return counts of elements on a table column depending on elements on another column
Hi,
I am given the following table:
> head(hsa_refseq)
chr genome region start stop nu strand nu.1 nu.2
gene_id
1 chr1 hg19_refGene CDS 67000042 67000051 0 + 0 gene_id
NM_032291
2 chr1 hg19_refGene exon 66999825 67000051 0 + . gene_id
NM_032291
3 chr1 hg19_refGene CDS 67091530 67091593 0 + 2 gene_id
NM_032291
4 chr1 hg19_refGene exon 67091530 67091593 0 + . gene_id
NM_032291
5 chr1 hg19_refGene CDS 67098753 67098777 0 + 1 gene_id
NM_032291
6 chr2 hg19_re...
2017 Aug 22
2
splitting a dataframe in R based on multiple gene names in a specific column
...ld appreciate please a suggestion on how to do the following :
i'm working with a dataframe in R that contains in a specific column
multiple gene names, eg :
> df.sample.gene[15:20,2:8]
Chr Start End Ref Alt Func.refGene
Gene.refGene284 chr2 16080996 16080996 C T ncRNA_exonic
GACAT3448 chr2 113979920 113979920 C T ncRNA_exonic
LINC01191,LOC100499194465 chr2 131279347 131279347 C G
ncRNA_exonic LOC440910525 chr2 223777758 223777758 T
A exonic AP1S3626 chr3 99794575 99794575 G
A exonic COL8A...
2017 Aug 23
0
splitting a dataframe in R based on multiple gene names in a specific column
Hi Bogdan,
Messy, and very specific to your problem:
df.sample.gene<-read.table(
text="Chr Start End Ref Alt Func.refGene Gene.refGene
284 chr2 16080996 16080996 C T ncRNA_exonic GACAT3
448 chr2 113979920 113979920 C T ncRNA_exonic LINC01191,LOC100499194
465 chr2 131279347 131279347 C G ncRNA_exonic LOC440910
525 chr2 223777758 223777758 T A exonic AP1S3
626 chr3 99794575 99794575 G A exonic COL8A1
643 chr3 132601066 132601066 A...
2011 Nov 15
1
Problem with substr
...ect, tmp.end[ex]
+ 1, tmp.start[ex + 1] - 1) :
invalid substring argument(s)
Could someone figure out what the problem is?
for(i in 1:length(genebody[,1])){
tmp.id<-as.vector(genebody[i,1]) # get gene id
tmp.subject<-as.vector(genebody[i,2]) # get gene sequence
tmp.exons<-exons[which(exons[,1]==tmp.id),] # get exons of the
selected genes
tmp.pattern<-as.vector(tmp.exons[,3]) # define exons as patterns
for alignment
tmp.align<-pairwiseAlignment(pattern=tmp.pattern,
subject=tmp.subject,type="local") # align all exons pairwise...
2011 Jun 27
1
create a new data frame after comparing two columns of the previous data frame
...o filter a table; If I am given for example the
following table:
> head(intra)
chr miRNA start end strand ACC hsa_ID
region region_start region_end gene_id transcrip_id
1 chr1 miRNA 1102484 1102578 + ACC="MI0000342"; ID="hsa-mir-200b";
exon 1102484 1102578 NR_029639 NR_029639
2 chr1 miRNA 1103243 1103332 + ACC="MI0000737"; ID="hsa-mir-200a";
exon 1103243 1103332 NR_029834 NR_029834
3 chr1 miRNA 1104385 1104467 + ACC="MI0001641"; ID="hsa-mir-429";
exon 110438...
2006 Jul 10
1
R newbie
Hello,
I am new to R and still feeling my way thru it.
I am trying to plot the values from this file below on the X-axis of a plot. I
have attached the graph to the email...the one i am trying to recreate.
Exon start end
5'UTR 22540060 22540121
1 22540122 22540140
2 22540303 22540493
3 22541552 22541565
4 22542373 22542519
5 22544265 22544432
3'UTR 22544433 22544856
I would like to create small rectangles on the x-axis as colored boxes from
start position to end position of each exon...with the...
2012 Mar 08
1
Correlation analysis for an exon array
Dear All,
I have an exon array and did not find any differential gene expression between two samples. I was looking to perform correlation analysis on the same. Can anyone recommend any package that would do this for an affy exon array?
Will SAM analysis give me correlated genes?
Thanks and regards,
Ekta
The information...
2008 Sep 11
1
subscript out of bounds
I'm working on Human Exon Array 1.0 ST. I'm getting normalized data
fine but I'm running into problems with QC. QCReport gives me the
following error:
> load(file= "huex10stv2cdf.rda")
> exon.data at cdfName <- "huex10stv2cdf"
> QCReport(exon.data, file = "QCReport.pdf...
2009 Oct 28
0
[BioC] Is there a package similar to mogene10stprobeset.db by for Affymetrix Exon Arrays?
mogene10stprobeset.db is generated with AnnotationDbi for mouse gene
array. I don't find a package that seems generated by AnnotationDbi
for exon arrays on the webpage you mentioned. Is it correct?
On Tue, Oct 27, 2009 at 7:00 PM, Marc Carlson <mcarlson at fhcrc.org> wrote:
> Hi Peng,
>
> I am not completely clear from your post what you want. ?But most of our
> annotation packages can be found here:
>
> http://www.b...
2008 Feb 21
3
variable syntax problem
...("ENSG00000115252", rma.affy, gps=list(1:3, y:z),
type="mean-int", gp.col=c("red", "blue"), by.order=TRUE,
scale.to.gene=FALSE, use.symbol=TRUE, use.mt=FALSE, *main="PDE1A
(red=prostate, blue=tissues[i])"*, ylab="intensity / probeset",
exon.y=1, exon.height=1, exon.bg.col="#c3c3c3",
exon.bg.border.col="black", show.introns=TRUE)
y=y-3
z=z-3
dev.off() }
when i write main=tissues[i] the value is written right. but i would
like to have an additional text...
thanks
paul
[[alternative HTML version deleted]]
2010 Apr 29
1
merged files
Hi,
i have two files (file1.txt and file2.txt) which i would like to merge,
based on certain criteria, i.e.
it combines data based on matching geneID and exons.
i have used the merge option, but it does not give me the desired outcome.
merged.txt shows the result i would like.
*File1. txt*
**
AffyProbe ProbeType Flag GeneSymbol GeneID Exons Chrom Strand Affytart
AffyEnd 1 1007_s_at:1105:483 0 0 DDR1 780 21 6 + 30975403 30975427 2
1007_s_at:111...
2010 May 11
3
Improving loop performance
...e to the p1 and ags1 vectors, which I have done, but this doesn't seem to improve speed much. Would anyone be able to provide me with advice on how I might be able to speed this up?
p1 <- character(dim(aga2)[1])
ags <- character(dim(aga2)[1])
for (i in 1:dim(aga2)[1])
{
if (aga2$first.exon[i]==TRUE)
{
p1[i]<-as.character(aga2[i, "AP"])
ags[i]<-as.character(aga2[i, "AS"])
}
else
{
p1[i]<-paste(p1[i-1], aga2[i, "AP"], sep=",")
ags[i]<-paste(ags[i-1], aga2[i, "AS"], sep=",")
}
}
Thanks.
--Mark Lam...
2014 Dec 05
2
[LLVMdev] [RFC] Semantic changes in the Metadata/Value split
> On 2014 Dec 5, at 10:53, Peter Collingbourne <peter at pcc.me.uk> wrote:
>
> On Fri, Dec 05, 2014 at 09:35:22AM -0800, Duncan P. N. Exon Smith wrote:
>>
>>> On 2014-Dec-05, at 00:39, Peter Collingbourne <peter at pcc.me.uk> wrote:
>>>
>>> On Thu, Dec 04, 2014 at 06:44:36PM -0800, Duncan P. N. Exon Smith wrote:
>>>> As of Monday, I finally got a preliminary patch passing check and...
2016 Mar 24
2
[RFC] Lazy-loading of debug info metadata
On Thu, Mar 24, 2016 at 6:35 AM, Duncan Exon Smith <dexonsmith at apple.com>
wrote:
>
>
> On Mar 24, 2016, at 6:22 AM, Teresa Johnson <tejohnson at google.com> wrote:
>
>
>
> On Wed, Mar 23, 2016 at 11:06 PM, Duncan P. N. Exon Smith <
> dexonsmith at apple.com> wrote:
>
>>
>> > On 2...
2014 Dec 05
3
[LLVMdev] [RFC] Semantic changes in the Metadata/Value split
> On 2014-Dec-05, at 00:39, Peter Collingbourne <peter at pcc.me.uk> wrote:
>
> On Thu, Dec 04, 2014 at 06:44:36PM -0800, Duncan P. N. Exon Smith wrote:
>> As of Monday, I finally got a preliminary patch passing check and
>> check-clang with the metadata-value split.
>
> Do you have the Go bindings enabled? Because of the changes you made to the
> DIBuilder interface, I expect that your changes will break the bind...
2016 Mar 25
1
[RFC] Lazy-loading of debug info metadata
On Thu, Mar 24, 2016 at 6:35 PM, Duncan P. N. Exon Smith <
dexonsmith at apple.com> wrote:
>
> > On 2016-Mar-24, at 12:58, Teresa Johnson <tejohnson at google.com> wrote:
> >
> >
> >
> > On Thu, Mar 24, 2016 at 6:35 AM, Duncan Exon Smith <dexonsmith at apple.com>
> wrote:
> >
> >
&g...
2010 Apr 29
1
Using plyr::dply more (memory) efficiently?
...tes manually w/o ddply by
using a combo of lapply and a do.call(rbind, ...) uses considerably
less ram (tops out at about 8GB).
How can I use ddply more efficiently?
Longer:
Here's more info:
* The data.frame itself ~ 15.8 MB when loaded.
* ~ 400,000 rows, 8 columns
It looks like so:
exon.start exon.width exon.width.unique exon.anno counts
symbol transcript chr
1 4225 468 0 utr 0
WASH5P WASH5P chr1
2 4833 69 0 utr 1
WASH5P WASH5P chr1
3 5659 152 38 utr...
2018 Jun 23
4
RFC: Should SmallVectors be smaller?
> On Jun 23, 2018, at 10:14, Chris Lattner <clattner at nondot.org> wrote:
>
>
>
>> On Jun 23, 2018, at 9:11 AM, Duncan P. N. Exon Smith <dexonsmith at apple.com <mailto:dexonsmith at apple.com>> wrote:
>>
>>>
>>> I think we might be better off just reducing the pre-allocation size of most of our SmallVectors across LLVM and Clang. They're all wild guesses, never profiled. Especially f...