In variani/athaliana: Functions to work with the A. thaliana data set

opts_chunk$set(fig.path = "docs/figures/", comment = NA, tidy = F, message = F, warning = F, echo = F, results = 'verbatim')

library(ggplot2)
library(pander)

library(devtools)
load_all()

theme_set(theme_light())
panderOptions('table.split.table', Inf)
panderOptions('knitr.auto.asis', FALSE)

athaliana

About

athaliana is an R data package for the A. thaliana data set https://github.com/Gregor-Mendel-Institute/atpolydb.

Data preparation

Files to download:

| Data | File name | Url | |:-----|:------------|:----| | phen. | athaliana_filename_phen() | athaliana_url_phen() | | SNP | athaliana_filename_snp() | athaliana_url_snp() |

R commands to download:

athaliana_download_phen(method = "wget")
athaliana_download_snp(method = "wget")

R commands to put data in a proper format:

athaliana_write_snp()
athaliana_write_map()       

snp <- athaliana_snp()
relmat <- athaliana_compute_relmat(snp, center = TRUE, scale = TRUE)
athaliana_write_relmat(relmat, filename = "relmat_centered.rds")

Code examples

A simple polygenic model

Here we are inerested to run a polygenic model (the lme4qtl R package) for one of the traits (FRI).

phen <- athaliana_phen(traits = "FRI")
relmat <- athaliana_relmat(filename = "relmat_std.rds")

library(lme4qtl)
(m <- relmatLmer(FRI ~ (1|id), phen, relmat = list(id = relmat)))

Note that the residuals are not OK.

r <- residuals(m)

qqnorm(r)
qqline(r)

hist(r, breaks = 30)

That likely means the trait needs to be transformed.

hist(phen$FRI, breaks = 30)

variani/athaliana documentation built on May 3, 2019, 4:34 p.m.