implementing new organizational structure

MarineOmics · Mar 20, 2023 · 572f6d0 · 572f6d0
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diff --git a/.DS_Store b/.DS_Store
diff --git a/.Rhistory b/.Rhistory
@@ -292,3 +292,17 @@ print(paste0("The number of SAMPLES in data: ", length(c(SeqArray::seqGetData(gd
 print(paste0("The number of SNPs in data: ",  length(c(SeqArray::seqGetData(gdsin, "variant.id")))))
 vcftools --vcf POP_02_RADseq/OL_subset.vcf --missing-indv --out POP_02_RADseq/OL_subset
 vcftools --vcf POP_02_RADseq/OL_subset.vcf --missing-indv --out POP_02_RADseq/OL_subset
+library(SeqArray) # efficient storage and filtering of genomic data
+library(tidyverse) # plotting data formatting and manipulation
+library(SNPRelate) # PCA and other popgen analyses
+gdsin = SeqArray::seqOpen(filename.gds)
+filename = "OL_subset" #replace with y our file name
+filename.gds = paste0("POP_02_RADseq/", paste0(filename, ".gds"))
+filename.vcf = paste0("POP_02_RADseq/", paste0(filename, ".vcf"))
+# 1 . Convert VCF to GDS
+SeqArray::seqVCF2GDS(vcf.fn = filename.vcf, out.fn = filename.gds, storage.option="ZIP_RA")
+gdsin = SeqArray::seqOpen(filename.gds)
+sample.ids = seqGetData(gdsin, "sample.id")
+knitr::include_graphics("ADMIN_01_submissions_instructions_files/Rivera_etal_fig.png")
+getwd
+getwd()
diff --git a/ADMIN_01_submissions_instructions.Rmd b/ADMIN_01_submissions_instructions.Rmd