# User:Timothee Flutre/Notebook/Postdoc/2012/02/29

Project name | Main project page Previous entry Next entry |

## Use R to extract the best SNP among all in cis of any given geneThis can be reformulated more generically as "extract one row for each level of a column based on the value of a second column": Let's create a dummy dataset: x <- data.frame("g"=c("g2","g1","g2","g1"), "s"=c("s1","s2","s3","s4"), p=c(10^-4,10^-3,10^-2,10^-5)) Here is how it looks like: g s p 1 g2 s1 1e-04 2 g1 s2 1e-03 3 g2 s3 1e-02 4 g1 s4 1e-05 For instance, the "g" column indicates gene names, the "s" column indicates SNP names, and the "p" column indicates P-values of association between genotypes at the SNP and variation in gene expression levels. In such a case, I want to extract the best SNP for each gene, ie. those with the lowest P-value. First, I sort the "g" column according to the P-values and I keep the row indices after sorting: v <- x$g[i <- order(x$p)] v [1] g1 g2 g1 g2 i [1] 4 1 2 3 Second, I find the first occurrence of each level in column "g" (in this example, the first occurrence corresponds to the lowest P-value for this gene): min.occ <- !duplicated(v) min.occ [1] TRUE TRUE FALSE FALSE Third, I retrieve the row indices corresponding to these first occurrences per level: row.idx <- setNames(seq_len(nrow(x))[i][min.occ], v[min.occ]) row.idx g1 g2 4 1 Finally, I extract the data I'm interested in: x[row.idx,] g s p 4 g1 s4 1e-05 1 g2 s1 1e-04 This could also be done more simply by: x[i[min.occ],] g s p 4 g1 s4 1e-05 1 g2 s1 1e-04 And according to this answer on SO, the whole procedure seems pretty fast! |