search for: snp

Displaying 20 results from an estimated 44 matches for "snp".

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2006 Apr 26
help in R
Hi, I cant understand where I am going wrong.Below is my code.I would really appreciate your help. Thanks. > genfile<-read.table("c:/tina/phd/bs871/hw/genfile.txt",skip=1) > > #read in SNP data > snp.dat <- as.matrix(genfile) > <- scan("c:/tina/phd/bs871/hw/genfile.txt",nline=1,what="character") Read 100 items > n.snp <- length( > <- 1 #number of fields for ids, sex and affection status > >...
2013 Jan 03
Index out SNP position
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 <- matrix(c(35838396,35838674,36003908,36004090,36150188,36151202,35838584,35838674,36003908,36003992), ncol = 2) B <- matrix(c(36003918,35838399,35838589,36262559),ncol...
2007 Jan 10
Fw: Memory problem on a linux cluster using a large data set [Broadcast]
...sensitive to big-data issues and tracking down > unnecessary memory copying. > > > "cannot allocate vector size 1240 kb". I''ve searched through > > use traceback() or options(error=recover) to figure out where > this is actually occurring. > > > SNP <- read.table("file.txt", header=FALSE, sep="") # > read in data file > > This makes a data.frame, and data frames have several aspects > (e.g., automatic creation of row names on sub-setting) that > can be problematic in terms of memory use. Probably be...
2013 Jan 04
FW: Index out SNP position
...ect. That way you are not modifying B. This will be faster than checking the order of the columns in A each time you process a line from B. > Ax <- t(apply(A, 1, function(x) c(min(x), max(x)))) > indx <- sapply(1:nrow(B), function(i) any(B[i]>Ax[,1] & B[i]<Ax[,2])) > SNP <- B[indx] > SNP [1] 36003918 35838399 35838589 -------------------- David C > From: JiangZhengyu [mailto:zhyjiang2006 at] > Sent: Friday, January 04, 2013 9:03 AM > To: dcarlson at > Subject: RE: [R] Index out SNP position > > Hi David, > >...
2013 Nov 08
SNPRelate: Plink conversion
Hi, Following my earlier posts about having problems performing a PCA, I have worked out what the problem is. The problem lies within the PLINK to gds conversion. It seems as though the SNPs are imported as "samples" and in turn, the samples are recognised as SNPs: >snpsgdsSummary("chr2L") Some values of snp.position are invalid (should be > 0)! Some values of snp.chromosome are invalid (should be finite and >=1)! Some of snp.allele are not standard! E.g,...
2010 Mar 05
Error in inherits(x, "data.frame") : subscript out of bounds
...n I wrote it but now it seems not to, and gives an error message: Error in inherits(x, "data.frame") : subscript out of bounds In addition: There were 50 or more warnings (use warnings() to see the first 50) warnings() Warning messages: 1: In corrs[j] <- cbind(expressions[j, 1:5], SNP.expr.cor) : number of items to replace is not a multiple of replacement length which indicates that the problem is with getting correlation and other information into corrs. cbind(expressions[j,1:5], SNP.expr.cor) is type data.frame. Changing corrs into matrix, dataframe, list or any other...
2011 Dec 13
snpStats imputed SNP probabilities
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 vi...
2003 Oct 19
jail + devfs + snp problem (FreeBSD 5.1-RELEASE-p10)
...ttyvd ptyp5 ptype ptypn ttyid1 ttyp6 ttypf ttypo ttyv5 ttyve Everything looks great, but: shell# w -n USER TTY FROM LOGIN@ IDLE WHAT root pm ??? ??? - w -n shell# jexec 1 /bin/sh # cd /dev # ls -al snp* ls: snp*: No such file or directory # watch -W pm shell# id uid=0(root) gid=0(wheel) groups=0(wheel), 5(operator) And I''m outside !
2005 Nov 05
problem with the assignment function
...uot;rhopair", which calls a .C function. I cannot assign its value to a variable using either "=" nor "<-". After I did the assignment, "rhopair" cannot reproduce the same result as before with the same argument. Here is the code and results: > rhopair(x=SNP,bp=bpp[1:700],A=93,B=BB) [1] 0.1012352 > rhopair(x=SNP,bp=bpp[1:700],A=93,B=BB) [1] 0.1012352 > a=rhopair(x=SNP,bp=bpp[1:700],A=93,B=BB) > a [1] 0.004524671 > rhopair(x=SNP,bp=bpp[1:700],A=93,B=BB) [1] 5.241946e-06 > a=rhopair(x=SNP,bp=bpp[1:700],A=93,B=BB) > a [1] 0.00...
2012 Jan 26
Request for help on manipulation large data sets
Dear All, I would like to ask for help on how to read different files automatically and do analysis using scripts. 1. Description of the data 1.1. there are 5 text files, each of which contains cleaned data for the same 100 SNPs. Observations (e.g., position on gnome, alelle type, ...) for SNPs are rows ordered by the SNP numbers, 1.2. there are 1 text file, containing the expression level of mRNAs 9 (and other information), which are rows ordered by mRNA numbers, So for each SNP the sample size is 5. 2. Description...
2007 Apr 23
Dominance in qtl model
Hi, I''m using R for a QTL analysis of SNP data. I was wondering if anyone had any advice on fitting a dominance effect into the following function; > myfun4 function (x) { x <- scan(con, nmax=169) y <- unique(x[which(!]) if(length(y)>1) { summary(lme(Ad ~ x, random= ~1|sire, na.action="na.omit")) } else {pri...
2013 Jan 05
package metafor: error when setting 'col' and 'at' for a forest plot
I am using metafor to create forest plots. This code gives me the expected plot (setting x axis tick marks): forest(forest$OR,$Low, ci.ub=forest$High, at=log(c(.05, .25, 1, 10)), slab=forest$SNP, atransf=exp) As does this (setting colors): forest(forest$OR,$Low, ci.ub=forest$High, col=c(1,2,3), slab=forest$SNP, atransf=exp) But if I try to set both ''at'' and ''col'': forest(forest$OR,$Low, ci.ub=forest$High, col=c(1,2,3), at=...
2011 Sep 26
Packages for snp, CNV data
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
2008 Aug 21
Need Functional SAP APO DP and SNP
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 Managem...
2018 Mar 05
Help with apply and new column?
...spersed, and some code at the end. On Mon, 5 Mar 2018, Sariya, Sanjeev wrote: > Thanks. I think nabble is good for programming questions. Bear with me > if I'm incorrect. You may have found R-help archives at Nabble, but R-help has nothing to do with Nabble. > > Data: Genomics SNP information I know almost nothing about using R for genomics. > Goal: I need to add Chromosome and SNP position to the data frame I'm using through apply. > > I'd like to add new column from text processed through apply function. > > For example: 10:60523:T:G (Column 2) &...
2013 Oct 03
prcomp - surprising structure
Hello, I did a pca with over 200000 snps for 340 observations (ids). If I plot the eigenvectors (called rotation in prcomp) 2,3 and 4 (e.g. plot (rotation[,2]) I see a strange "column" in my data (see attachment). I suggest it is an artefact (but of what?). Suggestion: I used prcomp this way: prcomp (mat), where mat is a matri...
2009 Nov 09
Using something like the "by" command, but on rows instead of columns
Hello R Forum users, I was hoping someone could help me with the following problem. Consider the following "toy" dataset: Accession SNP_CRY2 SNP_FLC Phenotype 1 NA A 0.783143079 2 BQ A 0.881714811 3 BQ A 0.886619488 4 AQ B 0.416893034 5 AQ B 0.621392903 6 AS B 0.031719125 7 AS NA 0.652375037 "Accession" = individual plants, arbitrarily identified by uni...
2018 Mar 05
Help with apply and new column?
Thanks. I think nabble is good for programming questions. Bear with me if I'm incorrect. Data: Genomics SNP information Goal: I need to add Chromosome and SNP position to the data frame I'm using through apply. I'd like to add new column from text processed through apply function. For example: 10:60523:T:G (Column 2) CHR: 10 Position: 60523 Dataset: chr rs ps n_miss allele1 allele0 af beta...
2010 Jun 14
error: subscript out of bounds?
Hi all, I want to get results for cox proportional hazards on SNP data. I''m trying to get HRs, CI''s, & p-values for each individual SNP - this is represented by cov[,i]. When I run my code, I get the following error: subscript out of bounds. I don''t know why I am getting this error. I have looked through the R logs, but nothing tha...
2007 Nov 30
about col in heatmap.2
Hi list, My data set is comprised of 47 columns and about 700 rows. Most of the values would be around 2, while some will go beyond in either direction, higher or lower. Is there a way to specify the parameter of col or others if necessary to have the range of representing colors be 0----8, and make dark for 2, red for higher than 2 and green for lower than 2. Is there a way to do this? Thanks a