This is a data package for running with the QTLseqr vignette. Please read the vignette here
For more information on running QTLseqr go to: https://github.com/bmansfeld/QTLseqr
he data is derived from: Mapping of Quantitative Trait Loci Underlying Cold Tolerance in Rice Seedlings via High-Throughput Sequencing of Pooled Extremes. Yang Z, Huang D, Tang W, Zheng Y, Liang K, et al. (2013) PLOS ONE 8(7): e68433. https://doi.org/10.1371/journal.pone.0068433
Raw reads were downloaded from the NCBI Short Read Archive, aligned to the v7 Nipponbare genome (http://rice.plantbiology.msu.edu/) and SNPs were called as described in the GATK “Best Practices” (https://software.broadinstitute.org/gatk/best-practices/).
You can install Yang2013data from github with:
# install.packages("devtools")
devtools::install_github("bmansfeld/Yang2013data")library("Yang2013data")
rawData <- system.file(
"extdata",
"Yang_et_al_2013.table",
package = "Yang2013data",
mustWork = TRUE)