I have this data as shown below .
Index / Name / Address / Chr / Position / GenTrain Score / 3999691203_R01C01 / 3999691203_R02C01
1 / exm-IND1-20 / 81717304 / 1 / 202183358 / 0.7119765 / AA / AA
2 / exm-IND1-83 / 41796243 / 1 / 85537661 / 0.8787801 /AA / AA
3 / exm-IND10-1 / 19664562 /10 / 102827757 / 0.7836018/ AB / AA
4 / exm-IND10-18 /90710943 / 10 / 18289633 / 0.8677844 / AA / AA
Name : it means the SNPs.
3999691203_R01C01 , 3999691203_R02C01, …. etc [column from 7 to 53] : those are the chip/sample number from microarray.
Through the manual script of SNPassoc (an R pachage to perform whole genome association )the following command was used : > myData.o<-setupSNP(SNPs, colSNPs=6:40, sort=TRUE, info=SNPs.info.pos, sep=“")
I have problem in the “ info” part. I can’t know what exactly i put instead of “SNPs.info.pos” to sort my SNP’s which is under the “Name “ column by chromosomes and genomic positions.
The example already have created an external data.frame “SNPs.info.pos” for the sorting issue. In my position, its already included in my data , its not not externally.
Can you please give me an advice or clue for solving my problem?
