I was going through the annotation of a 450K rnb.set object to have the position of 'rs' genotyping probes earlier today.
Following the documentation I did the following to get their coordinates on hg19:
genotyping.pb.hg19 <- annotation(rnb.set)[rownames(annotation(rnb.set)) %like% "rs", 1:3]
It contains a bed-like table with SNP IDs, Chromosome location, Start & End.
Since there is a "Start" and an "End" I though it was 0-based coordinates.
However, after checking in dbSNP the 1-based locations of SNPs match the 'Start' values.
Should'nt it match the 0-based 'End' value ?
I am not sure, but there might be a shift in 'rs' SNPs coordinates.
eg. rs3936238 is located on chr1:4131726 (1-based) in dbSNP.
However annotation() generates these 0-based coordinates (I did not included additionnal cols):
rs3936238 chr1 4131726 4131727
I would have expected something like this in 0-based instead:
rs3936238 chr1 4131725 4131726
Hi,
I was going through the annotation of a 450K rnb.set object to have the position of 'rs' genotyping probes earlier today. Following the documentation I did the following to get their coordinates on hg19:
genotyping.pb.hg19 <- annotation(rnb.set)[rownames(annotation(rnb.set)) %like% "rs", 1:3]It contains a bed-like table with SNP IDs, Chromosome location, Start & End. Since there is a "Start" and an "End" I though it was 0-based coordinates. However, after checking in dbSNP the 1-based locations of SNPs match the 'Start' values.
Should'nt it match the 0-based 'End' value ? I am not sure, but there might be a shift in 'rs' SNPs coordinates.
eg. rs3936238 is located on chr1:4131726 (1-based) in dbSNP. However
annotation()generates these 0-based coordinates (I did not included additionnal cols):rs3936238 chr1 4131726 4131727I would have expected something like this in 0-based instead:rs3936238 chr1 4131725 4131726Thank you in advance for the clarification.