similar to: Manhattan Plot

Hello, How can I run a backward stepwise regression with part of the variables fixed, while the others participate in the backward stepwise analysis? Thank you, Einat -- View this message in context: http://r.789695.n4.nabble.com/Stepwise-analysis-with-fixed-variables-tp4650015.html Sent from the R help mailing list archive at Nabble.com.

Hello all, I am trying to make a genome association plot for p-values related to SNPs and was fortunate to find that R contains a package that produces Manhattan plots which is what's preferred for my current project. The function mhtplot() is found in the 'gap' package which I installed in R 2.11.1 on Windows. I thought I'd test out the function first with the examples they

Hi R-ers, I am struggling with my x-axis in a association plot. What I would like is to place the labels of the x-axis between the tick markers and normally the labels are printed at the place where the tick marker is placed. I don???t want to move the tick marker (it gives the switch between one chromosome and the next) but I just want to put the chromosome number in between the

Hello All: I was wondering why many plot options are not working with mhtplot. I could not find much info about this function on the web too. Any comments, any detailed manual ... Thanks, MJK [[alternative HTML version deleted]]

Hi, As part of the bash 'shellshock' bug / vulnerability in unix/linux environments i would like to know whether the use of the samba parameter 'template shell' in my product may cause my product to be vulnerable to the shellshock bug , since this 'template shell' parameter , as per my understanding allows to open a remote bash session used by external users. I would

Hi, I'm using samba version 3.0.37 and i encountered a very strange and annoying phenomena when 2 different users from 2 different machines are getting the same PID from samba. (2 windows users that are trying to view documents on the CIFS share). I did some google research on this problem and i found the following regarding such a problem: " One can find references to problems like

To whom it may concern: My name is Jillian Weinfeld. I am currently and undergraduate student at New York University and working at Mount Sinai School of Medicine doing research with epilepsy patients. At the moment I am creating a manhattan plot with my data set. After reading many forums and such, I have appropriately plotted my data, however, I wanted to see how I can change the colors of the

R folks, I am trying to create a mhtplot plot that will alter the point size via the plot point value. The size of the point should change via a set criteria such as: if point value <10^-6 size 3x else if 10^-3> point value >10^-6 size 2x else point value >10^-3 size is x I consider myself an R newbie, and I am assuming that I could do this via some sort of function to change

Hello, Can anyone please suggest any packages in R that can be used to overlay gene expression data on SNP (affymetrix) copy number ? Thanks, Ekta Senior Research Associate Bioinformatics Department Jubilant Biosys Pvt Ltd, #96, Industrial Suburb, 2nd Stage Yeshwantpur, Bangalore 560 022 Ph No : +91-80-66628346 The information contained in this electronic message and in any attachments to this

Hi, I've noticed an issue with S4 methods and namespaces which only arises in particular, difficult to reproduce configurations. One example is the ggbio package in Bioconductor, which currently emits these warnings when its namespace is loaded: ---------------------- library(ggbio) Loading required package: ggplot2 Attaching package: ‘ggbio’ The following object(s) are masked from

Hi I've successfully installed Duke Nukem Manhattan Project, but when I try to start it, it prompts for the CD, although the CD is in the drive and the drive is set up properly in Wine settings. It seems people have run the game successfully on wine, so perhaps someone's got a clue about this issue. Thanks for any help!

Hi, Tenfei, I have two group of data composed of gene mutation and deletion on specific sites. Will it be possible for me to use the Manhattan Plot for comparison? Thank you for you attention! Li-Wu Guo, Ph.D. Sent from Windows Mail [[alternative HTML version deleted]]

Greetings, I am reaching out to this mailing list with the following job opportunity. It is with a high-volume, heavy-traffic web property based in Manhattan. The job description is below. If interested please send an updated resume to nathan.madsen@algomod.com Regards, Nathan Madsen Algomod Technologies Corporation 116 John Street New York, NY 10038 Job # :

Dear All, Thank you kindly for such detailed replies. I was looking to overlay data using algorithms so that i am able to tell which genes are differentially expressed due to changes in copy number. I did a pubmed search and found only 7 literature pieces all of which use in-house algorithms. I am yet to explore Gviz since it wouldn't work on R 2.14, would try it after upgrading to R 2.15.

Dear R users, When I run the following code, R crashes: require(cclust) x <- matrix(c(0,0,0,1.5,1,-1), ncol=2, byrow=TRUE) cclust(x, centers=x[2:3,], dist="manhattan", method="kmeans") While this works: cclust(x, centers=x[2:3,], dist="euclidean", method="kmeans") I'm posting this here because I am not sure if it is a bug. I've been searching

Hi, I want to merge multiple chromosomal regions based on their common intersecting regions. I tried couple of things using while and if loops but did not work out. I would appreciate if anyone could provide me a small piece of code in R to get the intersection of following example: chr1: 100-150 chr1: 79-250 chr1: 100-175 chr1: 300-350 I want the intersection of all four regions as follow:

Hi, I'm trying to make a chromosomal map in R by using the locus. I have a list of genes and their locus, and I want to visualise that so you can see if there are multiple genes on a specific place on a chromosome. A example of what I more or less want is below: http://www.nabble.com/file/p21474206/untitled.JPG untitled.JPG The genes and locus are here:

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:

Hi, I have a set of genes and its chromosomal physical position in a text file. I want to view those genes in the chromosome using R package GenePlotter. Could any one please tell how to view this. Thanks in advance. Yours sincerely, S.Mahalakshmi [[alternative HTML version deleted]]

I'm trying to identify the positions of all genes within a specific chromosomal region using biomart. When using the current biomart database I'm able to do this without issue. However, I need to use build 36 of the mouse genome which was last included in ensembl mart 46. I selected this mart and the mouse dataset as follows: mart<-useMart(biomart="ensembl_mart_46",