I need some advice and suggestion due to my problem, I am sorry if this question seems easy but I am beginner here to use r/qtl packages in R software. I have around 1000 markers (genotype) and 1 phenotype (100 data). I tried to run it used scannone with methode "mr"
However the data showed like this,
Here is my scripts,
data_mr <- read.csv("trial2.csv")
data_mr <- read.cross("csvr", file="trial2.csv", estimate.map=FALSE)
data_mr <- jittermap(data_mr, amount= .0001)
data_mr <- calc.genoprob(data_mr, step=0,eror.prob=0.01)
data.scanone <- scanone(data_mr, pheno.col = 1)
permulation.test <- scanone(data_mr, method = "em",
pheno.col = 1, n.perm=10)
I only have genotype data like "AA/BB" and do not have position of marker in cM. Are there any ways to make the chromosome name could be easy to distinguish? or do I have a mistake to input the data?
Thank you so much before.