Last updated: 2021-03-30

Checks: 2 0

Knit directory: R_gene_analysis/

This reproducible R Markdown analysis was created with workflowr (version 1.6.2.9000). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

R Markdown file: up-to-date

Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.

Repository version: e1faf81

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.

The results in this page were generated with repository version e1faf81. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated: 


Ignored files:
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/

Untracked files:
    Untracked:  data/Brec_R1.txt
    Untracked:  data/Brec_R2.txt
    Untracked:  data/CR15_R1.txt
    Untracked:  data/CR15_R2.txt
    Untracked:  data/CR_14_R1.txt
    Untracked:  data/CR_14_R2.txt
    Untracked:  data/KS_R1.txt
    Untracked:  data/KS_R2.txt
    Untracked:  data/NBS_PAV.txt.gz
    Untracked:  data/NLR_PAV_GD.txt
    Untracked:  data/NLR_PAV_GM.txt
    Untracked:  data/PAVs_newick.txt
    Untracked:  data/PPR1.txt
    Untracked:  data/PPR2.txt
    Untracked:  data/SNPs_newick.txt
    Untracked:  data/bac.txt
    Untracked:  data/brown.txt
    Untracked:  data/cy3.txt
    Untracked:  data/cy5.txt
    Untracked:  data/early.txt
    Untracked:  data/flowerings.txt
    Untracked:  data/foregeye.txt
    Untracked:  data/height.txt
    Untracked:  data/late.txt
    Untracked:  data/mature.txt
    Untracked:  data/motting.txt
    Untracked:  data/mvp.kin.bin
    Untracked:  data/mvp.kin.desc
    Untracked:  data/oil.txt
    Untracked:  data/pdh.txt
    Untracked:  data/protein.txt
    Untracked:  data/rust_tan.txt
    Untracked:  data/salt.txt
    Untracked:  data/seedq.txt
    Untracked:  data/seedweight.txt
    Untracked:  data/stem_termination.txt
    Untracked:  data/sudden.txt
    Untracked:  data/virus.txt
    Untracked:  output/GAPIT/GAPIT.FarmCPU.Pred.result.csv
    Untracked:  output/GAPIT/GAPIT.FarmCPU.Yield.Df.tValue.StdErr.csv
    Untracked:  output/GAPIT/GAPIT.FarmCPU.Yield.GWAS.Results.csv
    Untracked:  output/GAPIT/GAPIT.FarmCPU.Yield.MAF.pdf
    Untracked:  output/GAPIT/GAPIT.FarmCPU.Yield.Manhattan.Plot.Chromosomewise.pdf
    Untracked:  output/GAPIT/GAPIT.FarmCPU.Yield.Manhattan.Plot.Genomewise.pdf
    Untracked:  output/GAPIT/GAPIT.FarmCPU.Yield.QQ-Plot.pdf
    Untracked:  output/GAPIT/GAPIT.FarmCPU.Yield.phenotype_view.pdf
    Untracked:  output/GAPIT/GAPIT.GLM.Yield.Df.tValue.StdErr.csv
    Untracked:  output/GAPIT/GAPIT.GLM.Yield.GWAS.Results.csv
    Untracked:  output/GAPIT/GAPIT.GLM.Yield.Log.csv
    Untracked:  output/GAPIT/GAPIT.GLM.Yield.MAF.pdf
    Untracked:  output/GAPIT/GAPIT.GLM.Yield.Manhattan.Plot.Chromosomewise.pdf
    Untracked:  output/GAPIT/GAPIT.GLM.Yield.Manhattan.Plot.Genomewise.pdf
    Untracked:  output/GAPIT/GAPIT.GLM.Yield.Optimum.pdf
    Untracked:  output/GAPIT/GAPIT.GLM.Yield.PRED.csv
    Untracked:  output/GAPIT/GAPIT.GLM.Yield.QQ-Plot.pdf
    Untracked:  output/GAPIT/GAPIT.GLM.Yield.ROC.csv
    Untracked:  output/GAPIT/GAPIT.GLM.Yield.ROC.pdf
    Untracked:  output/GAPIT/GAPIT.GLM.Yield.phenotype_view.pdf
    Untracked:  output/GAPIT/GAPIT.MLM.Yield.Df.tValue.StdErr.csv
    Untracked:  output/GAPIT/GAPIT.MLM.Yield.GWAS.Results.csv
    Untracked:  output/GAPIT/GAPIT.MLM.Yield.Log.csv
    Untracked:  output/GAPIT/GAPIT.MLM.Yield.MAF.pdf
    Untracked:  output/GAPIT/GAPIT.MLM.Yield.Manhattan.Plot.Chromosomewise.pdf
    Untracked:  output/GAPIT/GAPIT.MLM.Yield.Manhattan.Plot.Genomewise.pdf
    Untracked:  output/GAPIT/GAPIT.MLM.Yield.Optimum.pdf
    Untracked:  output/GAPIT/GAPIT.MLM.Yield.PRED.csv
    Untracked:  output/GAPIT/GAPIT.MLM.Yield.QQ-Plot.pdf
    Untracked:  output/GAPIT/GAPIT.MLM.Yield.ROC.csv
    Untracked:  output/GAPIT/GAPIT.MLM.Yield.ROC.pdf
    Untracked:  output/GAPIT/GAPIT.MLM.Yield.phenotype_view.pdf
    Untracked:  output/GAPIT/GAPIT.MLMM.Pred.result.csv
    Untracked:  output/GAPIT/GAPIT.MLMM.Yield.Df.tValue.StdErr.csv
    Untracked:  output/GAPIT/GAPIT.MLMM.Yield.GWAS.Results.csv
    Untracked:  output/GAPIT/GAPIT.MLMM.Yield.MAF.pdf
    Untracked:  output/GAPIT/GAPIT.MLMM.Yield.Manhattan.Plot.Chromosomewise.pdf
    Untracked:  output/GAPIT/GAPIT.MLMM.Yield.Manhattan.Plot.Genomewise.pdf
    Untracked:  output/GAPIT/GAPIT.MLMM.Yield.QQ-Plot.pdf
    Untracked:  output/GAPIT/GAPIT.MLMM.Yield.phenotype_view.pdf

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

These are the previous versions of the repository in which changes were made to the R Markdown (analysis/index.Rmd) and HTML (docs/index.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File Version Author Date Message
Rmd bd5506f Philipp Bayer 2021-03-29 missing commits
html dc50cad Philipp Bayer 2021-03-29 Build site.
Rmd d371690 Philipp Bayer 2021-03-29 wflow_publish(“analysis/index.Rmd”)
html 0961366 Philipp Bayer 2021-03-24 Build site.
Rmd e747dc6 Philipp Bayer 2021-03-24 wflow_publish(files = c(“analysis/index.Rmd”, “analysis/yield_lm_link.Rmd”,
html da418d6 Philipp Bayer 2020-12-14 Build site.
Rmd bf5f9a7 Philipp Bayer 2020-12-14 wflow_publish(“analysis/index.Rmd”)
html e519122 Philipp Bayer 2020-12-11 Build site.
html 364fc37 Philipp Bayer 2020-12-11 Build site.
html 737c38c Philipp Bayer 2020-12-11 Build site.
Rmd 5d1b0ae Philipp Bayer 2020-12-11 analysis/yield_link.Rmd
html fa5c0ff Philipp Bayer 2020-11-04 Build site.
Rmd eae4c49 Philipp Bayer 2020-11-02 Broken link
html cfa0225 Philipp Bayer 2020-11-02 Build site.
Rmd 596689b Philipp Bayer 2020-11-02 wflow_publish(“analysis/index.Rmd”)
Rmd dae157b Philipp Bayer 2020-09-24 Update of analysis
html dae157b Philipp Bayer 2020-09-24 Update of analysis
Rmd 1b346e9 Philipp Bayer 2020-09-22 More data!
html 1b346e9 Philipp Bayer 2020-09-22 More data!
html 0777e1d Philipp Bayer 2020-09-22 update
Rmd 3adcc5a Philipp Bayer 2020-09-22 wflow_git_commit(all = TRUE)
html e6e9b9b Philipp Bayer 2020-09-21 Build site.
Rmd c71005a Philipp Bayer 2020-09-18 lots changes
html c71005a Philipp Bayer 2020-09-18 lots changes
html 7d33bac Philipp Bayer 2020-09-18 Build site.
Rmd 695db1e Philipp Bayer 2020-09-18 wflow_publish(c(“analysis/eda.Rmd”, “analysis/first-analysis.Rmd”,
html ca65f66 Philipp Bayer 2020-09-18 Build site.
Rmd efd6af1 Philipp Bayer 2020-09-18 wflow_git_commit(all = T)
html efd6af1 Philipp Bayer 2020-09-18 wflow_git_commit(all = T)
Rmd 7b1cd32 Philipp Bayer 2020-09-17 wflow_git_commit(all = T)
Rmd 8a6560a Philipp Bayer 2020-09-17 Start workflowr project.

Welcome to the website summarising the soybean R-gene analysis.

  1. EDA of PAV and different classes: link

  2. Plotting of NBS/RLK/RLP plots based on total numbers: link. These results are the main part of the paper.

  3. Linking yield with NLR gene counts using regular lm(): link. These results are the main part of the paper.

  4. GWAS using NLR genes link

DIRECTOR’S CUT

  1. Plotting of NBS/RLK/RLP plots based on percentage lost: link. These results are mostly not in the paper.

  2. Linking yield with NLR gene counts using lme4: link. These results are not in the paper, but informed the main part.