## ----风格，回声=假，结果='ASIS'-------------------------- - knitr：：opts_chunk $ set（eval = as.logical（sys.getenv（“knitr_eval”，“true”）），cache = as.logical（sys.getenv（“knitr_cache”，“true”））选项（宽度= 75）## ----消息=假------------------------------------------------图书馆（readr）库（doplt）## ---- eval = false ---------------------------------------------------------如果（！qualocamespace（“biocmanager”，静静= true））## install.packages（“biocmanager”）## ---- eval = false -------------------------------------------------- ## Biocmanager ::安装（C（“readr”，“doltr”））## ---- eval =错误的 - - - - - - - - - - - - - - - - - - - - - - - - ------- ## pdata_file < - file.choose（）## ---- echo = false ---------------------------------------------------------- system.file（package =“biocintro”，“extdata”，“all-Sample-Sheet.csv“）## ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- pdata ## --------------------------------------------------------------------------- pdata %>% arrange(age) ## ------------------------------------------------------------------------ pdata %>% arrange(desc(age)) ## ------------------------------------------------------------------------ pdata %>% summarize(n = n()) ## ---- eval = FALSE------------------------------------------------------- ## pdata %>% group_by(sex) ## ------------------------------------------------------------------------ pdata %>% group_by(sex) %>% summarize(n = n()) ## ---- eval = FALSE------------------------------------------------------- ## pdata %>% t.test(age ~ sex, data = .) ## ------------------------------------------------------------------------ pdata %>% group_by(mol.biol) %>% count() ## ------------------------------------------------------------------------ c("a", "b", "c", "b", "a") %in% c("a", "c") ## ---- message = FALSE---------------------------------------------------- library(ggplot2) ## ------------------------------------------------------------------------ ggplot(pdata, aes(x = sex, y = age)) ## ------------------------------------------------------------------------ ggplot(pdata, aes(x = sex, y = age)) + geom_boxplot() ## ------------------------------------------------------------------------ ggplot(pdata, aes(x = sex, y = age)) + geom_boxplot() + geom_jitter(width = .1, height = 0) ## ------------------------------------------------------------------------ sequences <- c("AAATCGA", "ATACAACAT", "TTGCCA") ## ------------------------------------------------------------------------ sequences length(sequences) nchar(sequences) sequences[c(1, 3)] sample(sequences) ## ---- eval=FALSE--------------------------------------------------------- ## reverseComplement(sequences) ## ------------------------------------------------------------------------ my_sequence <- "All the world's a stage, And all the men and women merely players" ## ---- message = FALSE---------------------------------------------------- library(Biostrings) ## ---- eval = FALSE------------------------------------------------------- ## if (!requireNamespace("BiocManager", quietly = TRUE)) ## install.packages("BiocManager") ## BiocManager::install("Biostrings") ## library(Biostrings) ## ------------------------------------------------------------------------ dna <- DNAStringSet(sequences) dna ## ------------------------------------------------------------------------ class(dna) ## ------------------------------------------------------------------------ fa_file <- system.file(package="Biostrings", "extdata", "dm3_upstream2000.fa.gz") ## ------------------------------------------------------------------------ readLines(fa_file, 5) ## ------------------------------------------------------------------------ tail(readLines(fa_file, 44), 5) ## ------------------------------------------------------------------------ dna <- readDNAStringSet(fa_file) dna ## ------------------------------------------------------------------------ gc <- letterFrequency(dna, "GC", as.prob = TRUE) ## ------------------------------------------------------------------------ gc <- dna %>% letterFrequency("GC", as.prob = TRUE) %>% tibble::as_tibble() gc ## ------------------------------------------------------------------------ sessionInfo()