Nothing
## ---- include = FALSE---------------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
## ---- message = FALSE---------------------------------------------------------
library(hlaR)
library(tidyverse)
library(dplyr)
## ---- message = FALSE---------------------------------------------------------
# use the testing data in the library
dat_mhc1 <- read.csv(system.file("extdata/example", "MHC_I_test.csv", package = "hlaR"), sep = ",", header = TRUE)
re_mhc1 <- CalEpletMHCI(dat_mhc1)
re_mhc1_single <- re_mhc1$single_detail
re_mhc1_overall <- re_mhc1$overall_count
## ---- message = FALSE---------------------------------------------------------
# use the testing data in the library
dat_mhc2 <- read.csv(system.file("extdata/example", "MHC_II_test.csv", package = "hlaR"), sep = ",", header = TRUE)
re_mhc2 <- CalEpletMHCII(dat_mhc2)
re_mhc2_single <- re_mhc2$single_detail
re_mhc2_overall <- re_mhc2$overall_count
re_mhc2_drdq_risk <- re_mhc2$dqdr_risk
## ----visualize mm-------------------------------------------------------------
hist(re_mhc1_overall$mm_cnt_tt)
hist(re_mhc2_overall$mm_cnt_tt)
mm_eplets <- strsplit(re_mhc1_single$mm_eplets, split = ",")
mm_eplets <- as.data.frame(matrix(as.factor(unlist(mm_eplets))))
colnames(mm_eplets) <- c("eplets")
count<- mm_eplets %>%
group_by(eplets) %>%
summarize(count=n())
count %>%
arrange(desc(count)) %>%
top_n(10) %>%
ggplot(aes(eplets, count)) +
geom_col()
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