README.md

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

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

R commands to put data in a proper format:

athaliana_write_snp()
athaliana_write_map()       

snp <- athaliana_snp()
relmat <- athaliana_compute_relmat(snp)
athaliana_write_relmat(relmat)

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()

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

Linear mixed model fit by REML ['lmerMod']
Formula: FRI ~ (1 | id)
   Data: phen
REML criterion at convergence: 328.4603
Random effects:
 Groups   Name        Std.Dev.
 id       (Intercept) 0.4524  
 Residual             0.4926  
Number of obs: 164, groups:  id, 164
Fixed Effects:
(Intercept)  
      1.182

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.

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