search for: exons

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 start end 413077 ChrX_133594175_133594368_HPRT1 193 ChrX 133594175 133594368 413270 ChrX_13359418...

If row numbers can be dispensed with, then tidyr makes this easy with the unnest function: ##### library(dplyr) #> #> Attaching package: 'dplyr' #> The following objects are masked from 'package:stats': #> #> filter, lag #> The following objects are masked from 'package:base': #> #> intersect, setdiff, setequal, union library(purrr)

...777 0 + . gene_id NM_032291 What I've done is to find out how many of the elements on 3rd column are "CDS", "exon". sum(hsa_refseq$region=="CDS") sum(hsa_refseq$region=="exon") But what I would like is to print for each chromosome how many are exons and how many CDS. For example chr1 has 5 CDS and 2 exons chr2 has 10 CDS and 3 exons... Can you tell what should I add? Or if I am doing this wrong, how should I do it? Thank you, Regards, Nanami [[alternative HTML version deleted]]

I would 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

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

...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...

Hi everyone, I am trying to find a way to 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

...2519 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 label showing 1, 2 etc under each respective exon. The 5' and 3' UTR would be colored different from the exons 1-5. Any suggestions and ideas would greatly appreciated. Thank you Kiran ------------------------------------------------- This email is intended only for the use of the individual or entity to which it is addressed and may contain information that is privileged and confidential. If the read...

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 contained in this electronic message and in any attachments to this message

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") Error in as.vector(ans[[i]][, i.probes]) : subscript out of

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

dear members, i would like to write a variable in a plot title (main="") but i don't know the right syntax:(...i tried a lot of different ways without success. here my example: y=30 z=33 for (i in 10:length(tissue)) { png(filename = tissues[i], width = 1024, height = 768, pointsize = 12, bg = "white") gene.graph("ENSG00000115252", rma.affy, gps=list(1:3,

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:1119...

R-users, I have the following piece of code which I am trying to run on a dataframe (aga2) with about a half million records.  While the code works, it is extremely slow.  I've read some of the help archives indicating that I should allocate space 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

> 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

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 2016-Mar-22, at 19...

> 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

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: > > > > > > On Mar 24,...

Hi all, In short: I'm running ddply on an admittedly (somehow) large data.frame (not that large). It runs fine until it finishes and gets to the "collating" part where all subsets of my data.frame have been summarized and they are being reassembled into the final summary data.frame (sorry, don't know the correct plyr terminology). During collation, my R workspace RAM usage goes

> 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 for vectors of rel...