search for: snp4

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 3...

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 snp1 snp2 snp...

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...

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 SI...

...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 that are also represented i...

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 ID7 CC GG CT AA ID8 _ _ _ _ ID9 CT GG CC AG ID10 CC GG...

...in 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]]

...c(0,1,0,-1,-1,1,1,-1,0,1,1,0,0,1,0,-1,-1,NA,0,-1,0,0,1,0), nrow=3, dimnames = list( c("bob", "frita", "trudy"), c("snp1", "snp2", "snp3", "snp4", "snp5","snp6", "snp7", "snp8") ) ) # phenotype data - resistant or susceptible to zombie infection phenotype.data = matrix( c("bob", "frita", "trudy", "resistant"...