Attempting to use QTLseqR..learning :) about qtlseqr

[floschill]

Hi Shaker,
you probably tried executing the following code:

#load the package
library("QTLseqr")

#Set sample and file names
HighBulk <- "SRR834931"
LowBulk <- "SRR834927"
file <- "SNPs_from_GATK.table"

#Choose which chromosomes will be included in the analysis (i.e. exclude smaller contigs)
Chroms <- paste0(rep("Chr", 12), 1:12)

#Import SNP data from file
df <-
    importFromGATK(
        file = file,
        highBulk = HighBulk,
        lowBulk = LowBulk,
        chromList = Chroms
     )

This requires a table-file called "SNPs_from_GATK.table" in your working directory, which is not provided by QTLseqr when you just download and install the package. I would recommend reading the vignette (here), starting with the chapter "Standard workflow", that also describes how to download and use the Yang2013 example data.
Flo

[bmansfeld]

closed