search for: snp1

Hello I have two data frames, SNP4 and SNP1: > head(SNP4) Animal Marker Y 3213 194073197 P1001 0.021088 1295 194073197 P1002 0.021088 915 194073197 P1004 0.021088 2833 194073197 P1005 0.021088 1487 194073197 P1006 0.021088 1885 194073197 P1007 0.021088 > head(SNP1) Animal Marker x 3213 19407...

Why does the assignment of a 3178x93 object to another 3178x93 object remove the dimension attribute? > GT <- array(dim = c(6,nrow(InData),ncol(InSNPs))) > dim(GT) [1] 6 3178 93 > SNP1 <- InSNPs[InData[,"C1"],] > dim(SNP1) [1] 3178 93 > SNP2 <- InSNPs[InData[,"C2"],] > dim(SNP2) [1] 3178 93 > dim(pmin(SNP1,SNP2)) [1] 3178 93 > GT[1,,] <- pmin(SNP1,SNP2) > dim(GT) NULL # why?????????????????????????????????????? &g...

Hello all, I hope some of you can come to my rescue, yet again. I have two genetic datasets, and I want one of the datasets to have only the columns that are in common with the other dataset. Here is a toy example (my real datasets have hundreds of columns): Dataset 1: Individual SNP1 SNP2 SNP3 SNP4 SNP5 1 A G T C A 2 T C A G T 3 A C T C A Dataset 2: Individual SNP1 SNP3 SNP5 SNP6 SNP7 4 A T T G C 5 T A A G G 6 A A T C G I want Dataset1 to have only columns tha...

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 sir...

Hi Readers, I have a question. I have a large dataset and want to throw away columns that have the same value in the column itself and I want to know which column this was. For example > x<-data.frame(id=c(1,2,3), snp1=c("A","G", "G"),snp2=c("G","G","G"),snp3=c("G","G","A")) > x id snp1 snp2 snp3 1 1 A G G 2 2 G G G 3 3 G G A Now I want to know that snp2 in monom...

Hi, I have a large dataset on which I would like to do the following: x<-data.frame(id=c(1,2,3), snp1=c("AA","GG", "AG"),snp2=c("GG","AG","GG"),snp3=c("GG","AG","AA")) > x id snp1 snp2 snp3 1 1 AA GG GG 2 2 GG AG AG 3 3 AG GG AA And then reshape the datase...

Hi, I've got a quite tricky question. I have a txt file, named 'temp.txt', as the following: snp1 snp2 snp3 AA 00 00 GG GG 00 00 AA 00 I want to read the file into R. 1) when I use 'read.table' without 'header=T' option, > temp <- read.table('temp.txt') # I got > temp V1 V2 V3 1...

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...

Hi, I'm using libvirt(1.0.0) with python, for managing virtual machines.. but while taking multiple snapshot domain is crashing... Snapshot XML ------------------------- <domainsnapshot> <name>snp1</name> <creationTime></creationTime> <description>Description</description> <state></state> <domain> <uuid></uuid> </domain> <parent> <name></name> </parent> </domainsnapshot> ---...

Hi, I have a question about the data handling. I have a dataset as following: ID snp1 snp2 snp3 1001 0/0 1/1 1/1 1002 2/2 3/3 1/1 1003 4/4 3/3 2/2 I want to convert the dataset to the following format: ID snp1 snp2 snp3 1001 00 AA AA 1002...

I am trying to use the survfit() function with the newdata argument to produce predicted survivor curves for a particular covariate profile. The main purpose of the plot will be to visualise the effect of snp1, coded 0 and 1. In my Cox model I have stratified by one variable, edu, and so I know I will automatically get a separate curve for each strata. My problem is how to deal with the variable sitenew, which is a 3 level factor (coded 0,1,2). coxsnps$edu <- as.factor(coxsnps$edu) coxsnps$sitene...

...new to a fit that contained that variable as a factor. (Perhaps it should be smart enough to at least die gracefully -- but it's not). The simple solution is to not use factors. site1 <- 1*(coxsnps$sitenew==1) site2 <- 1*(coxsnps$sitenew==2) test1 <- coxph(Surv(time, censor) ~ snp1 + sex + site1 + site2 + gene + eth.self + strata(edu), data= coxsnps) output profile1 <- data.frame(snp1=c(0,1), site2=c(0,0), sex=c(0,0), site1=c(0,0), site2=c(0,0), geno=c(0,0) eth.self=c(0,0)) plot(survfit(test1, newdata=profile1)) Note that you do not have to ex...

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 SN...

...Aa=1 and AA=2) aa Aa AA case 2 3 0 control 2 2 0 So I should not use this one or if I am using it, then I need to see 0 0 in to AA column which I don't see when I use the table command in R. snpmat category SNP1 SNP2 SNP3 .... SNPN case 1 0 2 1 case 0 1 1 2 case 1 2 2 0 control 0 1 0 1 con...

I'm new to R (previously used SAS primarily) and I have a genetics data frame consisting of genotypes for each of 300+ subjects (ID1, ID2, ID3, ...) at 3000+ genetic locations (SNP1, SNP2, SNP3...). A small subset of the data is shown below: SNP_ID SNP1 SNP2 SNP3 SNP4 Maj_Allele C G C A Min_Allele T A T G ID1 CC GG CT AA ID2 CC GG CC AA ID3 CC GG nc AA ID4 _ _ _ _ ID5 CC GG CC AA ID6 CC GG CC AA...

...urs,( at a later point of time It should be possible to revert to the actual domain state when I took the snapshot), I'm using libvirt APIs python bindings, there are many flags defined, so which way I can accomplish it..? as of now I"m using flag value as zero. API Call -------------- snp1=domain1.snapshotCreateXML(snp_xml,0) virDomainSnapshotCreateFlags enum virDomainSnapshotCreateFlags { VIR_DOMAIN_SNAPSHOT_CREATE_REDEFINE = 1 Restore or alter metadata VIR_DOMAIN_SNAPSHOT_CREATE_CURRENT = 2 With redefine, make snapshot current VIR_DOMAIN_SNAPSHOT_CREATE_NO_METADATA = 4 Make sna...

...text-file, line by line, evaluate it and write it back into a textfile in a different position; Phenotypeinfo.txt (contains phenotype information) Before.txt (contains genotypeinformation -see below-) SNP;1-305,000 ID:1-900 allele.A alleleB After.txt (the required format) ID:1-250 phenotype SNP1.allelA SNP1.alleleB SNP2.Allele.A SNP2.allele.B etc I have been looking at ?read.table/scan/readline/SQL-light but have not resolved it. Should I refer to PERL or can this be tackled? I am using a windows machine with R 2.6.0 Any help would be highly appreciated, Many Thanks, Marco

...ulate SNP interactions. I have a list of 100 SNPs, I need to look at the interaction between each of two SNPs among the list. my question is how to perform this in GenABEL. I want to use the "lm" function, but don't know how to use the SNP information. for example: result <- (lm(y~SNP1+SNP2+SNP1*SNP2)) the problem here is the "SNP1,SNP2" are not working in this place, because it's not a right format to use the SNP information stored in the GenABEL library. Someone said I could first import the GenABEL format genetic data to the format used by "genetics" li...

...enotype) for certain number of individuals and creating a loop that will randomly simulate it for 10000 times *(permutation)*. I also need to find how I keep the information (p value for each SNP) gathered for all the 10000 iterations. My data set looks like this (n=500): Individual # Phenotype SNP1 SNP2 SNP3 SNP4 SNP5 SNP6 SNP7 SNP8 SNP9 SNP10 SNP11 SNP12 1 0 T T G G A C G T A A T C 2 1 A T C G A C G T A G T C Many thanks, Jonathan [[alternative HTML version deleted]]

...at phdata', it's easy to add these rows, but for 'gwaa at gtdata', I think I need to create SNP data as '0 0 0 0 0.....' for all the dummy parents first. I am using the function 'convert.snp.ped', so I need a 'pedfile' of this format: #ped id fa mo sex trait snp1.allele1 snp1.allele2 snp2.allele1 snp2.allele2 ...# 1 1 0 0 1 2 0 0 0 0 ... 1 2 0 0 1 0 0 0 0 0 ... 1 3 0 0 2 1 0 0 0 0 ... . . 100 101 0 0 2 1 0 0 0 0 ... If we use the 1M microarray, usually, after QC, there will be ~800 thousands SNPs, so this file is really huge. I created this matrix in R, a...