search for: chrom

...and its more of a learning exercise for myself than anything else, but I'm stuck and getting extremely frustrated that I can't figure it out. I'm trying to make a fairly simple figure, but also trying to make it look "better" using ggplot2. I have data.frame that contains chrom length 1 chr1 249250621 2 chr2 243199373 3 chr3 198022430 4 chr4 191154276 5 chr5 180915260 6 chr6 171115067 7 chr7 159138663 8 chrX 155270560 9 chr8 146364022 10 chr9 141213431 11 chr10 135534747 12 chr11 135006516 13 chr12 133851895 14 chr13 115169878 15 chr14...

...1680 35 5 chr2 21750 84 6 chr2 21820 29 7 chr2 31890 46 8 chr3 32100 29 9 chr3 52380 29 10 chr3 66450 46 I would like to insert the following 4 lines at the beginning: browser position chr1:1-10000 browser hide all track type=wiggle_0 name=sample description=chr1_sample visibility=full variableStep chrom=chr1 span=1 and then insert 2 lines before each chromosome: track type=wiggle_0 name=sample description=chr2_sample visibility=full vriableStep chrom=chr2 span=1 The final result should be tab delimited file that looks like this: browser position chr1:1-10000 browser hide all track type=wiggle_0 na...

...ll.tf7[i-1,6]+1) x<-as.numeric(all.tf7[i,2]) } else if (all.tf7[i,1]!=all.tf7[i-1,1]) { all.tf7[i,6]<-(all.tf7[i-1,6]+1) x<-as.numeric(all.tf7[i,2]) } } #the aim here is to attribute a bin number to each row so that I can then split the dataframe according to those bins. chrom chromStart chromEnd name cumsum bin chr1 10089 10309 ZBTB33 10089 1 chr1 10132 10536 TAF7_(SQ-8) 20221 1 chr1 10133 10362 Pol2-4H8 30354 1 chr1 10148 10418 MafF_(M8194) 40502 1 chr...

...on was a vector containing the codes identifying the RNA sequences, and libname was a vector containing the codes identifying the tissue sample (library)." The structure of my data is as follows: R> structure(list(cyto = c("A", ?B?, ?C?, ?D?), nuc = c(?A?, ?B?, ?E?, ??), chrom = c(?B?, ?F?, ??, ??)),.Names = c("cyto", "Nuc", "chrom")) accession should be "A", "B",.... and libname schould be "cyto", "nuc" and "chrom" as I understand it... Could you help me? Sorry, that might be a very...

Hi, I'm trying to match peaks between chromatographic runs. I'm able to match peaks when they are chromatographed with the same method, but not when there are different methods are used and spectra comes in to play. While searching I found the ALS package which should be usefull for my application, but I couldn't figure it out. I m...

I've got two tables.... first one(table1): ID chrom start end Ex1 2 152 180 Ex2 10 2000 2220 Ex3 15 3000 4000 second one ( table2): chrom location name 2 160 Alv 2 190...

Dear list, I wish to plot chromatin precipitation data: I would like to have a rectangles (x:end-start, y:peak) but I do not have an idea how to define x (in terms of qplot syntax) and to choose the correct geom. mydata is a subset of a larger file. > mydata chrom start end peak 1 chr11 5291000 5291926 8...

On Fri, 16 Jan 2009, r-help-request at r-project.org wrote: > Date: Thu, 15 Jan 2009 13:29:03 +0100 > From: Pablo G Goicoechea <pgoikoetxea at neiker.net> > Subject: Re: [R] How to create a chromosome location map by locus ID > To: Sake <tlep.nav.ekas at hccnet.nl> > Cc: r-help at r-project.org > Message-ID: <496F2C0F.3040304 at neiker.net> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Sake: > If you do not find an answer within the li...

...; > 主题: Re: Bayesian Hidden Markov Models > 收件人: "monkeylan" <[hidden email]> > 日期: 2012年2月28日,周二,下午7:02 > > > Dear James, > > Basically you just need the values (y) and the positions (in your case it > would be the index of the times series). The chromosome argument does not > apply to your case so it can be a vector of ones. > If the positions are at the same distance between (equally spaced) then the > model will be homogeneous. > > So for example something like this would be enough: >> library(RJaCGH) >> y &lt...

...n (#). I do not know how to do that in R. Could you please give helps on this problem? Thanks in advance. Best, Jian-Feng, ################################################################## The lines I want to write in the header lines look like, with words in the last line (here the line "#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001") be separated by tab : ##fileformat=VCFv4.1 ##fileDate=20090805 ##source=myImputationProgramV3.1 ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta ##contig=<ID=20,length=62435964...

...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:1119:177 0 0 DDR1 780 21 6 + 30975549 30975573 3 1007_s_at:1136:469 0 0 DDR1 780 21 6 + 30975766 30975790 4 1007_s_at:192:205 0 0 DDR1 780 21 6 + 30975523 30975547 5 1007_s_at:474:1161 0 0 DDR1 780 21 6...

...solve the following error by reinstallation of the sqldf package. Can anyone suggest a different way to perform this kind of merge function? Thank you, Ding > DMRlog2pbde47DMS <- sqldf("select * from DMR_log2pbde47 as a left join DMS_log2pbde47 as b + on a.chrom = b.chromosome and a.start <= b.MAPINFO and a.end >= b.MAPINFO" ) Error in get(as.character(FUN), mode = "function", envir = envir) : object 'as.AsIs' of mode 'function' was not found --------------------------------------------------------------------- -SE...

Hello all, I'm trying to calculate the standar desviation and I'm using the function sd(x,na.rm=TRUE) and I have this error:? Error in var(x, na.rm = na.rm) : no complete element pairs . Why happen this?, What can I do to solve it?. x is list of three numbers which I have from a table. Thanks so much from Spain Carlos Morales Diego

...9;t happen with all of my data points (some do not have errors). Any ideas? Thanks, Sean function(x,annot,rat1,rat2,rf,...) { par(las=2) wh <- which(annot[,5]==x) xmax <- max(annot[wh,4]) xmin <- min(annot[wh,3]) chr <- annot[wh,2][1] wh.rf <- rf$chrom==as.character(chr) & rf$txStart>xmin & rf$txEnd<xmax par(mfrow=c(2,1)) plot(annot[wh,3],rat1[wh],type="l",xlab="",ylab="log2 Ratio",main=x,...) points(annot[wh,3],rat1[wh]) apply(rf[wh.rf,],1,function(z) { browser() i...

...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:1119:177 0 0 DDR1 780 21 6 + 30975549 30975573 3 1007_s_at:1136:469 0 0 DDR1 780 21 6 + 30975766 30975790 4 1007_s_at:192:205 0 0 DDR1 780 21 6 + 30975523 30975547 5 1007_s_at:474:1161 0 0 DDR1 780 21 6...

I have a data frame (narrow) with 431 rows and 6 columns containing information on chromosome, position, lod1, lod2, lod3, lod4, looking like this: > narrow chr pos lod1 lod2 lod3 lod4 1 1 3.456 -0.025 -0.003 -0.209 -0.057 2 1 5.697 -0.029 -0.005 -0.200 -0.058 3 1 8.434 -0.049 -0.012 -0.247 -0.092 4 1 9.466 -0.074 -0.025 -0.300 -0.136 5 1...

Hello R Developers I am using DNACopy package http://bioconductor.org/packages/1.9/bioc/html/DNAcopy.html I am not able to figure out how to (if at all possible) to modify output format, namely, I am getting the following: "ID" "chrom" "loc.start" "loc.end" "num.mark" "seg.mean" Is it a way to get also median and standard deviation? Thanks in advance, Vlad -- *********************************** Dr. Vladimir Makarov Instructor, Computer Science Department School of Computer Scie...

...l=1) for(j in 1:length(x)) { diversitym=read.table(paste(paste("Div-Chr",x[j], sep=""),"_corr.txt",sep=""), header=T, sep="\t", row.names=NULL) attach(diversitym) diversitytemp <- cbind(diversitytemp,diversitym) print(paste(paste("Diversity-Chrom",x[j], sep=""),".txt",sep="")) print(dim(diversitytemp)) } I am essentially trying to combine several tab-delimited text data files together into one big file. I recently upgraded to R 2.2.0. I now get multiple error messages of the form: The following object(s...

...(file='./plotST.eps',paper='special',width=10,height=10,horizontal=FALSE) > par(mfrow=c(5 ,1)) > plot(sortord , X1 , cex=0.5 ,pch=21 , ylim=c(1.000002 , 8.08771 ), xlab='ST: 1-5 position (unit)',ylab='ylabel',font.lab = 1, cex.lab = 1,cex.main=0.5 +0.4, col=chrom ) > text(midpointsbyc+minadj+5,0-5,chnum ,cex=0.5 +0.2 ,col=chnum+1 ) > abline(h = -1*log10(9.7e-08 ), lty = 2,col = 'gray' ) > # Draw the legend > legend('topright',legend=c('X1')) > plot(sortord , X2.... .... > # Put a box around the plot > box(...

...an to tweak it so I have some questions about why this works 1- The data I have has the date and time format as a single string like this "2006-04-09 10:20:00". But the code was set up to read the data in two columns ie- "2006-04-09" & "10:20:00". Is this how the chrom package expects to have the data, or is there a way I can change the code to read the data as a single column. For now I am chopping up my date and time data manually before I run R. 2- I've read the help on "as.is", and I'm not sure why I need that function in the first line of...