I'm using R/QTL to search for SNPs associated with several different phenotypes in double-haploid rainbow trout.
I've worked my way through R/QTL with general success, but have run into an issue when it comes to the genetic map. I have roughly 15,000 screened SNPs from an original set of about 100,000 RAD-seq Illumina SNP data across the 29 chromosomes for my organism, each of which was mapped to a high-density physical location (in BP) based on previous genomic work for the organism (example files attached email).
R/QTL sends up a warning when I read in the data and clearly knows that my locations are in BP rather than CM, but my solution of omitting the location row on my datasheet during the data read-in (and thus hoping that the program would assume location based on the order of the markers) results in a "Does Not Converge" warning (see below).
I wanted to ask if you might have a good suggestion for how to proceed. I found a number of FAQs, etc that suggested that using physical maps causes problems, but am not sure how to proceed. I'm not a geneticist by trade, but added a genetic component to my third dissertation chapter, for defense in late July. The FAQ for R/QTL seems to suggest that I need to build a linkage map De Novo, is that necessary for a basic QTL scan?
Any advice you might be able to offer would be enormously appreciated. I've attached the code that I'm using for the data read-in, example datasets, and the warnings produced for reference.
*******************Code & Errors*****************
QTL1.Length10C <- read.cross("csv", "","D:/FilteredSNP-Length10C-RQTL.csv", genotypes=c("A", "B"), crosstype="dh", estimate.map=TRUE)
--Read the following data:
87 individuals
14983 markers
2 phenotypes
--Estimating genetic map
--Cross type: dh
Warning message:
In summary.cross(QTL1.Length10C) :
Some chromosomes > 1000 cM in length; there may be a problem with the genetic map.
(Perhaps it is in basepairs?)
QTL1.Length10C <- read.cross("csv", "","D:/FilteredSNP-Length10C-RQTL-NOBP.csv", genotypes=c("A", "B"), crosstype="dh", estimate.map=TRUE)
--Read the following data:
87 individuals
14983 markers
2 phenotypes
--Estimating genetic map
--Cross type: dh
Warning messages:
1: In est.map(cross, error.prob = error.prob, map.function = map.function) :
Didn't converge!
2: In summary.cross(cross) :
Some chromosomes > 1000 cM in length; there may be a problem with the genetic map.
(Perhaps it is in basepairs?)