similar to: Need Functional SAP APO DP and SNP

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Hi I have a script which is designed to gather data from individual columns from a file, which is an output from an instrument. the file has multiple sections and each a section has data under each column (vars), I am using the name of the column as a variable to gather the column ID using vidx<-grep(vars[vi],gsub("[[:punct:]]","",strrl1[[datbeg-1]]),ignore.case=T) the

Hello, I would like to plot specific SNPs with their exact locations on a chromosome. Based on my genotyping results I would like to separate these SNPs in three different categories: 1, 2 and 3 and use different colours to represent these categories. The script below generates the sample data. I can plot these with the image function using the following: val <- 1:3 samp <- sample(val,

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

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:

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.

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

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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

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 <-

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

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

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]]

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