In fboehm/qtl2effects: Tools for Allele Effects at Established Quantitative Trait Loci

knitr::opts_chunk$set(dev="CairoPNG")

knitr::opts_chunk$set(echo = TRUE)

Read the files

load("../data/reduced_map_qtl2_mapping_objects.Rdata")
kinship <- qtl2::calc_kinship(probs = genoprobs.1, type = "loco")
nc <- 64

library(magrittr)
library(ggplot2)

Chr 7: KC, lung CFU

dat <- readr::read_csv("../data/pheno_clinical_4qtl2_win2_05OCT2019_v4.csv")
dmat <- as.matrix(dat[, -1])
rownames(dmat) <- dat$X1

sout <- qtl2::scan1(genoprobs = genoprobs.1, pheno = dmat, kinship = kinship, addcovar = addcovar)
qtl2::find_peaks(sout, map.1, threshold = 6) %>%
  dplyr::arrange(chr)
# KC peak: 20, lungCFU peak: 16

phe <- as.matrix(dat[, c("KC", "lungCFU")])
rownames(phe) <- dat$X1
start <- 1
end <- max(which(map.1$`7` < 30)) 

library(future.batchtools)
library(future)
plan("batchtools_multicore")

sp_out <- qtl2pleio::scan_pvl(probs = genoprobs.1$`7`, 
                                pheno = phe,
                              addcovar = addcovar,
                                kinship = kinship$`7`,
                                start_snp = start,
                                n_snp = end - start + 1)
(lrt <- qtl2pleio::calc_lrt_tib(sp_out))

sp_out %>%
  qtl2pleio::calc_profile_lods() %>%
  qtl2pleio::add_pmap(pmap = map.1$`7`) %>%
  ggplot2::ggplot() + ggplot2::geom_line(ggplot2::aes(x = marker_position, y = profile_lod, colour = trait))

Colophon

This report was generated on r Sys.time() using the following computational environment and dependencies:

# which R packages and versions?
if ("devtools" %in% installed.packages()) devtools::session_info()

The current Git commit details are:

# what commit is this file at? 
if ("git2r" %in% installed.packages() & git2r::in_repository(path = ".")) git2r::repository(here::here())  

fboehm/qtl2effects documentation built on Sept. 20, 2021, 7:34 p.m.