similar to: Plotting question: how to plot SNP location data?

Hello, I've searched for an answer to no avail. I am wondering if anyone knows how to constrain certain correlations to be equal. I have family data with 2 twins per family plus up to 2 siblings. I would like to somehow constrain all the sibling correlations (twin-sib and sib-sib) to be the same while allowing the twin-twin correlation to be different. Here is some simulated code:

I've recently moved from pxegrub to pxelinux (well, syslinux...) for many benefits. (memory fingerprint, etc) Its running perfectly, and exactly how I like it, except. LOCALBOOT 0 DOES NOT actually mount and boot the hard drive. All it seems to be doing is actually return error to the BIOS, which then boots the next device in it's list. This isnt a problem on most systems, but on

Hi, I was installing hundreds of packages on a machine with a single call to install.packages() and after a long time the call to install.packages() finally returned with the following warnings and errors: Warning messages: 1: packages ?hgu133aprobe?, ?hgu95av2.db?, ?BSgenome.Celegans.UCSC.ce2?, ?BSgenome.Mmusculus.UCSC.mm10?, ?BSgenome.Dmelanogaster.UCSC.dm3.masked?,

Hi, I have a data.frame like this: y <- rnorm(60) lev <- gl(3,20, labels=paste("lev", 1:3, sep="")) date1 <- as.Date(seq(ISOdate(2007,9,1), ISOdate(2007,11,5), by=60*60*24)) date1 <- date1[-c(3,4,15,34,38,40)] df <- data.frame(lev=lev, date1=date1, y=y) I would like to produce a new data.frame with missing days in df$date1 in each df$lev, like this: lev

Hi, Does anybody know how to obtain the imputed SNP genotype probabilities from the snpStats package? I am interested in using an imputation method implemented in R to be further used in a simulation study context. I have found the snpStats package that seems to contain suitable functions to do so. As far as I could find out from the package vignette examples and its help, it gives the

Hi, In addition to GADA, what are the available package in R and bioconductor to analyze amplification, deletion, LOH and indels of CNV, SNP data? Any reference is welcome. Best, Carol

I'm having trouble getting summaries out of the 250K snp chips in R. I'm using the oligo package and when I attempt to create the necessary SnpQSet object (to get genotype calls and intensities) using snprma, I encounter memory issues. Anyone have an alternative package or workaround for these large snp chips? -- View this message in context:

Hi ihave one table that look like SNP1 SNP2 SNP3 SNP4 SNP5 SIRE1 1 -1 -1 1 -1 SIRE2 1 -1 1 1 1 SIRE3 -1 -1 1 1 0 SIRE4 -1 1 1 0 1 SIRE5 -1 1 -1 -1 1 SIRE6 0 0 0 1 -1 SIRE7 -1 0 -1 1 1 SIRE8 1 -1 NA 0 NA SIRE9 -1 1 1 -1 -1 SIRE10 1 1 1 1 1 table 2 only one line SNP1 SNP2 SNP3 SNP4 SNP5 SIRE100 -1 -1 1 1 -1 I need to male

Dear all, I generated a dataset with 500 unrelated individuals and 10 biallelic SNPs. From this dataset,I would like to create data with 5% missingness on genotype information at random and also data with 5% genotyping error. Can someone help me with how I can do it. [[alternative HTML version deleted]]

When SEV is enabled in domcapabilities does that just mean any of SEV, SEV-ES, SEV-SNP is possible on the hardware? Similarly, does enabling SEV as a launchSecurity option in a domainXML mean that whichever SEV is available will be enabled? And if the guest policy has the ES flag set, it will not be created unless ES is enabled? Sorry if these questions don't make sense or are ill-formed.

Hello, I have indicators for the present of absent of a snps in columns and the categorey (case control column). I would like to extract ONLY the tables and the indices (SNPS) that give me 2 x 3 tables. Some gives 2x 2 tables when one of the allelle is missing. The data look like the matrix snpmat below: so the first snp should give me the following table: (aa=0, Aa=1 and AA=2) aa

Hi I am sure there is a function out there already but I couldn't find it. I have SNP data, that is, a matrix which contains in each row two characters (they are different in each row) and I would like to convert this matrix to a binary one according to the minor allele frequency. For non-geneticists: I want to have a binary matrix for which in each row the 0 stands for the less frequent

Hi , This is prabhu from levanture Inc. Our Tier1 vendor Needs Functional SAP APO DP and SNP Location:CA Duration:6+ Months Project is undergoing a change in company code for part of its business within USA. Such a change requires changes to our existing setup in SAP R/3 and SAP APO. The goal is to ensure business as usual post change in company code for Global Supply Chain Management

shell# /sbin/devfs rule -s 2 delset shell# /sbin/devfs rule -s 2 add hide shell# /sbin/devfs rule -s 2 add path random unhide shell# /sbin/devfs rule -s 2 add path urandom unhide shell# /sbin/devfs rule -s 2 add path zero unhide shell# /sbin/devfs rule -s 2 add path pty\* unhide shell# /sbin/devfs rule -s 2 add path pty\* unhide shell# /sbin/devfs rule -s 2 add path tty\* unhide shell#

I know that there are quite a few packages out that there for cluster analysis. The problem that I am facing is finding a package that will not incorporate all my samples into clusters but just the samples that fit a threshold (that I have not set yet and may need help finding the right level) for genotyping. It should be able to "no call" samples outside the clusters. It also needs to

Dear R helpers I have a table and i need to make new table table1: sire snp1 snp2 snp3 snp4 snp5 snp6 snp7 snp8 snp9 snp10 snp11 snp12 snp13 snp14 snp15 8877 -1 -1 -1 -1 0 0 -1 -1 -1 0 1 1 1 -1 -1 7765 1 1 1 0 0 0 -1 1 1 1 0 0 0 1 0 8766 1 1 -1 0 -1 -1 0 -1 0 -1 -1 -1 0 1 0 6756 0 1 0 -1 1 -1 -1 0 0 0 0 -1 0 1 1 5644 -1 0 1 -1 0 0 0 0 -1 -1 0 0 0 0 1 I have table2 sire

I think you mean between column 1 and 2 of A? Why is 36003918 not included? It is clearly between 35838396 and 36151202 in the first row of A. My earlier solution should work fine. Just create a new matrix AX that has the columns switched so that the start is always column 1 and use that to identify the ones you want to select. That way you are not modifying B. This will be faster than checking

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

Dear R experts, I have 2 matix: A& B. I am trying to index B against A - (1) find out B rows that fall between the col 1 and 2 of A& put them into a new vector SNP.I made code as below, but I cannot think of a right way to do it. Could anyone help me with the code? Thanks,Jiang---- A <-

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.