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index.Rmd
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---
title: "Home"
author:
- Costa, W. G.^[Weverton Gomes da Costa, Pós-Doutorando, Embrapa Mandioca e Fruticultura, wevertonufv@gmail.com]
date: "`r Sys.Date()`"
site: workflowr::wflow_site
url: https://wevertongomescosta.github.io/Genomic-Selection-for-Drought-Tolerance-Using-Genome-Wide-SNPs-in-Casava
output: workflowr::wflow_html
editor_options:
chunk_output_type: console
github-repo: wevertongomescosta/Genomic-Selection-for-Drought-Tolerance-Using-Genome-Wide-SNPs-in-Casava
---
This website is a project for analysis of the Genome Wide Association Studies (GWAS) for Drought Tolerance Using Genome Wide GBS and/or DART in Cassava by EMBRAPA Mandioca.
```{r}
geno <-
read.table("data/allchrAR08.txt", head = FALSE)
dim(geno)
geno[1:10,1:20]
write.table(geno, "geno.txt")
geno2 <- geno %>%
select(1, 2, which(geno[1,] %in% names$ID_Clone)) %>%
janitor::row_to_names(1) %>%
separate(alleles, c("REF", "ALT"))
geno3<-geno2 %>%
mutate_at(vars(4:20), ~ ifelse(.x == REF, 2, ifelse(
.x == ALT, 0, ifelse(.x != REF |
.x != ALT , "NA", 1)
)))
write.table(geno2,"geno2.txt", col.names = FALSE, row.names = FALSE)
dim(geno)
```