## ----load_package-------------------------------------------------------- library(clonotypeR) ## ----load_data----------------------------------------------------------- clonotypes <- read_clonotypes(system.file('extdata', 'clonotypes.txt.gz', package = "clonotypeR")) summary(clonotypes) ## ----clonotype_table----------------------------------------------------- head(clonotype_table(levels(clonotypes$lib), data=clonotypes)) head(clonotype_table(levels(clonotypes$lib), "V", data=clonotypes)) head(clonotype_table(levels(clonotypes$lib), "J", data=clonotypes)) ## ----yassai_identifier--------------------------------------------------- # Unique identifier head(yassai_identifier(clonotypes)) ## ----other_functions----------------------------------------------------- clonotypes <- clonotype_table(levels(clonotypes$lib), data=clonotypes) # First six clonotypes of library C head(unique_clonotypes("C", data=clonotypes)) # Count clonotypes found in library A, and B or C. length(common_clonotypes(group1="A", group2=c("B","C"), data=clonotypes)) # Matrix of numbers of common clonotypes common_clonotypes(data=clonotypes) ## ----load_data2---------------------------------------------------------- clonotypes <- read_clonotypes(system.file("extdata", "clonotypes2.tsv.xz", package = "clonotypeR")) ## ----summary_2----------------------------------------------------------- summary(clonotypes) ## ----explore_data2------------------------------------------------------- abc <- clonotype_table(c('A','B','C'), data=clonotypes) head(abc) summary(abc) ## ----explore_data2b------------------------------------------------------ abc[abc$C == 124, ] ## ----explore_data2v------------------------------------------------------ clonotype_table(c('A','B','C'), "V", data=clonotypes) head(clonotype_table(c('A','B','C'), c("V","J"), data=clonotypes))