Last updated: 2020-11-11
Checks: 7 0
Knit directory: IITA_EA_2020/
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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 |
|---|---|---|---|---|
| html | a58160e | wolfemd | 2020-11-11 | Build site. |
| Rmd | 8903c1c | wolfemd | 2020-11-11 | All code for processing and imputing DCas20_5251 for IITA-EA is ready to run. |
| html | 8903c1c | wolfemd | 2020-11-11 | All code for processing and imputing DCas20_5251 for IITA-EA is ready to run. |
| Rmd | 5514ab8 | wolfemd | 2020-10-09 | Ready for github |
| html | 5514ab8 | wolfemd | 2020-10-09 | Ready for github |
| html | 7efdd90 | wolfemd | 2020-10-09 | Build site. |
| html | c6022b6 | wolfemd | 2020-10-09 | Build site. |
| Rmd | 201e930 | wolfemd | 2020-10-09 | 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 IITA-EA imputation and related procedures.
From Morag: “there are five main parents in the CET trial and nine parents in PYT trial. The parents in CET are included in the 9 PYT parents. Nine main parents in PYT. Also in CET trial.”
So: from conversation in email, impute with E. Africa Imputation Reference Panel dataset, which can be found on the Cassavabase FTP server here with names e.g. chr*_ImputationReferencePanel_StageVI_91119.vcf.gz with code/documentation here.
Original report DCas20_5261 was not in format used for NextGen GS, i.e. a format that includes “counts” and ~VCF files. We were able to obtain a the right formats through Andrzej: OrderAppendix_1_DCas20-5261.
Steps:
Files:
chr*_ImputationReferencePanel_StageVI_91119.vcf.gzchr*_DCas20_5261_EA_REFimputed.vcf.gzchr*_DCas20_5261_EA_REFimputedAndFiltered.vcf.gzDosageMatrix_ImputationReferencePanel_StageVI_91119.rdsDosageMatrix_DCas20_5261_EA_REFimputedAndFiltered.rdsHOW 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_StageVI_91119.rds")
snps_dcas20_5261<-readRDS("DosageMatrix_DCas20_5261_EA_REFimputedAndFiltered.rds")
snps2keep<-colnames(snps_refpanel)[,colnames(snps_refpanel) %in% colnames(snps_dcas20_5261)]
snps<-bind_rows(snps_refpanel[,snps2keep],
snps_dcas20_5261[,snps2keep])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/IITA_EA_2020/ with all data.
NOTICE: data/ and output/ are empty on GitHub. Please see ftp://ftp.cassavabase.org/marnin_datasets/IITA_EA_2020/ for access.
data/: raw data (e.g. unimputed SNP data)output/: outputs (e.g. imputed SNP data)analysis/: most code and workflow documented in .Rmd filesdocs/: compiled .html, “knitted” from .RmdSupporting functions code/
The analyses in the html / Rmd files referenced above often source R scripts in the code/ sub-folder.
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_0.6.27 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_2.5 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