## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----installation, eval = FALSE----------------------------------------------- # install.packages("devtools") # devtools::install_github("TessaMacNish/HaploVar") ## ----message = FALSE, warning = FALSE, eval = TRUE---------------------------- library(HaploVar) ## ----load-data, eval = TRUE, include = FALSE---------------------------------- # Load data data("vcf") data("LD") ## ----load-vcf, eval = TRUE, include = TRUE------------------------------------ head(vcf, c(5,10)) ## ----load-LD, eval = TRUE, include = TRUE------------------------------------- head(LD, c(5,5)) ## ----define_haplotypes, message = F, results = 'hide', cache = T-------------- ##Run define_haplotypes haplotype_list <- define_haplotypes(vcf, LD, epsilon = 0.8) #this produces a list of haplotype tables haplotype_table <- haplotype_list[[1]] #this is the first haplotype tables ## ----head-haplotype-table, eval = TRUE, include = TRUE------------------------ head(haplotype_table, c(5,5)) ## ----collate_haplotype_list, message = F, results = 'hide', cache = T--------- ##Prepare the data haplotype_list2 <- haplotype_list #We are copying the haplotype_list so that we have two lists for the demonstration list_outputs <- list(haplotype_list, haplotype_list2) #The input must be in list format ##Run collate_haplotype_list collate_haplotype_list <- collate_define_haplotypes(list_outputs) ## ----define_haplotypes_globally, message = F, results = 'hide', cache = T----- ##Prepare the data vcf2 <- vcf vcf_list <- list(vcf, vcf2) #The vcf files must be in list format LD2 <- LD LD_list <- list(LD, LD2) #The LD matrices must be in list format ##Prepare parameters epsilon_list <- c(0.8, 0.8) #The length of this list must be the same as the number of vcf files. ## ----define_haplotypes_globally_2, message = F, results = 'hide', cache = T---- ##Run define_haplotypes_globally haplotype_list_global <- define_haplotypes_globally(vcf_list, LD_list, epsilon = epsilon_list) ## ----haplotype_variants, message = F, results = 'hide', cache = T------------- ##Run haplotype_variants format1 <- haplotype_variants(vcf, LD, epsilon = 0.8, format = 1) ## ----collate_haplotype_variants, message = F, results = 'hide', cache = T----- ##format1 format1B <- format1 format1_list <- list(format1, format1B) #The input for collate_haplotype_variants must be in list format. format1_collate <- collate_haplotype_variants(format1_list, format = 1) ## ----haplotype_variants_global, message = F, results = 'hide', cache = T------ format1_global <- haplotype_variants_global(vcf_list, LD_list, epsilon = epsilon_list, format = 1)