Last updated: 2020-10-09

Checks: 7 0

Knit directory: NaCRRI_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.


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.

Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.

The command set.seed(20200826) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.

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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 bcbcec3. 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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    Deleted:    analysis/convertDCas20_5360_ToVCF.Rmd

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/convertDCas20_5419_ToVCF.Rmd) and HTML (docs/convertDCas20_5419_ToVCF.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 c6022b6 wolfemd 2020-10-09 Build site.
Rmd 4f8a229 wolfemd 2020-10-09 Publish imputations for 2020 of DCAs20_5360 (and 2019 code too) for

Input Parameters

#' @dartvcfInput input name and path of "vcf" file from DArT
#' @dartcountsInput input name and path of counts file from DArT
#' @outName output path and name
#' @nskipvcf number of "VCF" rows to skip on read-in
#' @nskipcounts number of "counts file" rows to skip on read in
#' @ncores number of cores to use, could be VERY memory intensive
#' @dartVars chr vector, column names that _are not_ sample IDs in the read-counts file. I use this internally to assign the sampleIDs in the VCF file

library(tidyverse); library(magrittr)
dartvcfInput<-here::here("data/Report-DCas20-5419","Report_5419_VCF_Ref_Version6.txt")
dartcountsInput<-here::here("data/Report-DCas20-5419","Report_5419_Counts_Ref_Version6.csv")
outName<-here::here("data/Report-DCas20-5419","DCas20_5419")
nskipvcf<-2 
nskipcounts<-3
ncores<-10

Prelim. check format

Start manual. Check that the files read in according to previous code. Adjust code if necessary. Make a function and apply it to the input files.

# vcf<-read.table(dartvcfInput,
#                 stringsAsFactors = F,skip = nskipvcf, header = T, sep = "\t", comment.char = "")
# readCounts<-read.csv(dartcountsInput, stringsAsFactors = F,header = T,skip=nskipcounts)
# 
# dim(vcf)
# # [1] 13603  2052
# dim(readCounts)
# # [1] 27206  2068
# 
# # the lenghts don't match?
# 
# # Initial look at names....
# colnames(readCounts)[1:100]
#  #  [1] "AlleleID"                      "CloneID"                      
#  #  [3] "AlleleSequence"                "TrimmedSequence"              
#  #  [5] "TrimmedSequence_plus_Strand"   "Chrom_Cassava_v61"            
#  #  [7] "Tag_ChromPos_Cassava_v61"      "SNP_ChromPos_Cassava_v61"     
#  #  [9] "AlnCnt_Cassava_v61"            "AlnEvalue_Cassava_v61"        
#  # [11] "Strand_Cassava_v61"            "SNP"                          
#  # [13] "SnpPosition"                   "CallRate"                     
#  # [15] "OneRatioRef"                   "OneRatioSnp"                  
#  # [17] "FreqHomRef"                    "FreqHomSnp"                   
#  # [19] "FreqHets"                      "PICRef"                       
#  # [21] "PICSnp"                        "AvgPIC"                       
#  # [23] "AvgCountRef"                   "AvgCountSnp"                  
#  # [25] "RepAvg"                        "GS_Prediction_NaCRRI_2019_2"  
#  # [27] "GS_Prediction_NaCRRI_2019_1"   "GS_Prediction_NaCRRI_2019_26" 
#  # [29] "GS_Prediction_NaCRRI_2019_28"  "GS_Prediction_NaCRRI_2019_64" 
#  # [31] "GS_Prediction_NaCRRI_2019_77"  "GS_Prediction_NaCRRI_2019_92" 
#  # [33] "GS_Prediction_NaCRRI_2019_80"  "GS_Prediction_NaCRRI_2019_3"  
#  # [35] "GS_Prediction_NaCRRI_2019_14"  "GS_Prediction_NaCRRI_2019_52"
# colnames(vcf)[1:30]
# #  [1] "X.CHROM"                      "POS"                         
# #  [3] "ID"                           "REF"                         
# #  [5] "ALT"                          "QUAL"                        
# #  [7] "FILTER"                       "INFO"                        
# #  [9] "FORMAT"                       "GS_Prediction_NaCRRI_2019_2" 
# # [11] "GS_Prediction_NaCRRI_2019_11" "GS_Prediction_NaCRRI_2019_12"
# # [13] "GS_Prediction_NaCRRI_2019_13" "GS_Prediction_NaCRRI_2019_3" 
# # [15] "GS_Prediction_NaCRRI_2019_4"  "GS_Prediction_NaCRRI_2019_5" 
# # [17] "GS_Prediction_NaCRRI_2019_6"  "GS_Prediction_NaCRRI_2019_7" 
# # [19] "GS_Prediction_NaCRRI_2019_8"  "GS_Prediction_NaCRRI_2019_9" 
# # [21] "GS_Prediction_NaCRRI_2019_10" "GS_Prediction_NaCRRI_2019_1" 
# # [23] "GS_Prediction_NaCRRI_2019_23" "GS_Prediction_NaCRRI_2019_24"
# # [25] "GS_Prediction_NaCRRI_2019_25" "GS_Prediction_NaCRRI_2019_14"
# # [27] "GS_Prediction_NaCRRI_2019_15" "GS_Prediction_NaCRRI_2019_17"
# # [29] "GS_Prediction_NaCRRI_2019_18" "GS_Prediction_NaCRRI_2019_19"

# Need to add a check in the conversion function 
# that matches the names and reorders if necessary...

#... turns out, the function already checks for that!!  
# But seriously... the two outputs should come in the same order to avoid downstream problems.

Conversion function

Available and sourced from code/ subdirectory: convertDart2vcf.R.

Run conversion function

source(here::here("code/","convertDart2vcf.R"))
convertDart2vcf(dartvcfInput,dartcountsInput,outName,
                nskipvcf=2,nskipcounts=3,ncores)

Genomewide to per-chrom VCFs

Split the genome-wide VCF into per-chromosome VCFs for imputation.

require(furrr); options(mc.cores=18); plan(multiprocess)
source(here::here("code","imputationFunctions.R"))

vcfIn<-here::here("data/Report-DCas20-5419","DCas20_5419.vcf.gz")
filters<-"--minDP 4 --maxDP 50" # because using GT not PL for impute (Beagle5)
outPath<-here::here("data/Report-DCas20-5419/")
outSuffix<-"DCas20_5419"

future_map(1:18,
           ~splitVCFbyChr(Chr=.,
                          vcfIn=vcfIn,filters=filters,
                          outPath=outPath,outSuffix=outSuffix))

2043 clones, 12981 SNP


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_0.4.7      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_3.0.3    
[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