From c53d1f633468ae9193b0b95579765d2ebde922c3 Mon Sep 17 00:00:00 2001 From: Marc Galland Date: Thu, 13 Aug 2020 10:18:27 +0200 Subject: [PATCH] update test runs --- README.md | 20 +++++++++++--------- 1 file changed, 11 insertions(+), 9 deletions(-) diff --git a/README.md b/README.md index a88ae1d..1ea2416 100644 --- a/README.md +++ b/README.md @@ -22,8 +22,9 @@ Both methods will perform a Genome Wide Analysis (GWAS) using genetic variant (V - [Example datasets](#example-datasets) - [VCF dataset](#vcf-dataset) - [Phenotypes](#phenotypes) - - [Test run](#test-run) - - [Run the random_forest_gwas.R script](#run-the-random_forest_gwasr-script) + - [Test runs](#test-runs) + - [Random Forest](#random-forest-1) + - [RAINBOWR GWAS](#rainbowr-gwas) - [4. References](#4-references) - [:writing\_hand: Authors](#writing_hand-authors) - [vcfR](#vcfr) @@ -80,7 +81,7 @@ In the Shell, type `git clone https://github.com/SilkeAllmannLab/gwas.git` :tada: :confetti_ball: That's it! :tada: :confetti_ball: -# 3. Test +# 3. Test ## Example datasets @@ -128,14 +129,15 @@ done A `root_data_fid_and_names.tsv` file contains the genotype line identifier and the phenotypic values. Arabidopsis ecotypes were treated with 2-E-hexanal and their main root length measured. A response ratio was then calculated for each of the ecotypes by comparing the 2-E-hexanal treatment with a mock (methanol). -## Test run +## Test runs -## Run the random_forest_gwas.R script -- Open RStudio. -- In RStudio, select "File > New Project". -- Open the `gwas.R` script. -- Run the script. +### Random Forest +- Open a new Shell window. +- Execute the random forest script: `Rscript random_forest/gwas.R --help` to see the full list of arguments. +### RAINBOWR GWAS +- Open RStudio +- Run the `rainbowr/rainbowr.R` script. Make sure you specify a valid VCF file path and phenotype file. # 4. References