Last updated: 2020-10-17

Checks: 7 0

Knit directory: EMBRAPA_2020GS/

This reproducible R Markdown analysis was created with workflowr (version 1.6.2). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.


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The results in this page were generated with repository version d2fd3f7. 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:


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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 f309dea wolfemd 2020-10-17 Start workflowr project.
html fa3b6e1 wolfemd 2020-09-01 Build site.
html d97980a wolfemd 2020-09-01 Build site.
Rmd f3a0e16 wolfemd 2020-09-01 Added a link to cassavabase FTP destination for the data.
html d29d605 wolfemd 2020-09-01 Build site.
Rmd 6e27397 wolfemd 2020-09-01 EMBRAPA C2 has been imputed. Publish report and share to cassavabase
html ed70a5a wolfemd 2020-08-26 Build site.
Rmd 9d4dfab wolfemd 2020-08-26 Code organized into functions. Ready to run imputation of C2?
Rmd 4cc20db wolfemd 2020-08-26 Start workflowr project.
Rmd 245ee4f wolfemd 2020-08-26 Start workflowr project.

This repository and website documents all analyses, summary, tables and figures associated with EMBRAPA genomic prediction and related procedures (e.g. imputation).

Imputation 2019

Imputation conducted in 2019: Imputation of the L. America reference panel (GBS+DArTseqLD) and EMBRAPA GS C1 (DArTseqLD only) was done in October 2019. The codes for 2019 imputation were never published in a Git repository, though they were shared internally. The 2019 imputed VCFs will serve as imputation reference panel for 2020. Therefore, I am publishing the 2019 codes here as is for reference.

Imputation 2020

DArTseqLD (DCas20-5360) arrived on Aug. 22, 2020. Contains GS C2 for EMBRAPA.

STEPS:

FILES:

DOWNLOAD FROM CASSAVABASE FTP SERVER orDOWNLOAD (files <50Mb) FROM GitHub

Last year’s reference panel for imputation had ~64K SNP. The C1 progeny imputed by it had <9K SNP after post-imputation filters. Since imputation with Beagle5.0 is very fast, I imputed C2 (DCas20-5360) with three variants of the reference panel:

  1. Last year’s reference panel, without C1 (64K SNP)
  1. Last year’s ref. panel + C1 (include unfiltered C1 data = 64K refpanel SNP)

NOTICE: REFimputedWithC1unfiltered is not a good dataset. Chr. 4 is entirely filtered out, including using the “lighter” filter. This emphasizes that it is not a good idea to use poorly imputed haplotypes in the reference panel… evidenced also by the fact that the REFimputedWithC1filtered has markers passing filters on all chromosomes.

  1. Last year’s reference panel + C1 (reduce refpanel to sites passing post-impute filter in C1 = 9K SNP)

HOW TO COMBINE DOSAGE MATRICES: Users will want to combine the genotypes in the imputation reference panel files, with the genotypes in the imputed DArT file. They can have slightly different sets of markers along the columns. Here is a basic example how to combine:

snps_refpanel<-readRDS("DosageMatrix_ImputationReferencePanel_EMBRAPA_Phased_102619.rds")
snps_dcas20_5360<-readRDS("DosageMatrix_DCas20_5360_REFimputeLightFiltDR2pt3.rds")

snps2keep<-colnames(snps_refpanel)[,colnames(snps_refpanel) %in% colnames(snps_dcas20_5360)]
snps<-bind_rows(snps_refpanel[,snps2keep],
                snps_dcas20_5360[,snps2keep])

SUGGESTION: Use combination PCA, prediction, correlation of kinship matrices (off-diagonals and diagonals) to compare these datasets.

Data availability and reproducibility

The R package workflowr was used to document this study reproducibly.

Much of the supporting data and output from the analyses documented here are too large for GitHub.

The repository will be mirrored, here: ftp://ftp.cassavabase.org/marnin_datasets/EMBRAPA_2020GS/ with all data.

Directory structure of this repository

NOTICE: data/ and output/ are empty on GitHub. Please see ftp://ftp.cassavabase.org/marnin_datasets/EMBRAPA_2020GS/ for access.

  1. data/: raw data (e.g. unimputed SNP data)
  2. output/: outputs (e.g. imputed SNP data)
  3. analysis/: most code and workflow documented in .Rmd files
  4. docs/: compiled .html, “knitted” from .Rmd

Supporting functions code/

The analyses in the html / Rmd files referenced above often source R scripts in the code/ sub-folder. These are wrapper functions around the packaged core functions in predCrossVar, to do the specific analyses for this paper.


sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] workflowr_1.6.2

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.5       whisker_0.4      knitr_1.30       magrittr_1.5    
 [5] R6_2.4.1         rlang_0.4.8      stringr_1.4.0    tools_4.0.2     
 [9] xfun_0.18        git2r_0.27.1     htmltools_0.5.0  ellipsis_0.3.1  
[13] yaml_2.2.1       digest_0.6.25    rprojroot_1.3-2  tibble_3.0.4    
[17] lifecycle_0.2.0  crayon_1.3.4     later_1.1.0.1    vctrs_0.3.4     
[21] promises_1.1.1   fs_1.5.0         glue_1.4.2       evaluate_0.14   
[25] rmarkdown_2.4    stringi_1.5.3    compiler_4.0.2   pillar_1.4.6    
[29] backports_1.1.10 httpuv_1.5.4     pkgconfig_2.0.3