In uzh/ezRun: An R meta-package for the analysis of Next Generation Sequencing Data

knitr::opts_chunk$set(echo = FALSE)
library(ezRun)
## debug
#title: "`r paste(:'PBSV', params$sample`)"
#wddir <- "/srv/GT/analysis/qiwei/DNA-seq-202305/project3/sample_1"
wddir <- "."
#params = list(sample="sample_1")
## end of debug

Result {.tabset}

Genome Size

params$sample

dat.file <- file.path(wddir, paste0(params$sample,".kmer.freq.stat.final.genomic.characters"))
dat <- readLines(dat.file)
library(knitr)
cat(dat[c(19:22)], sep = '\n')

kmer frequency plot

svg.file <- file.path(wddir, paste0(params$sample,".kmer.freq.stat_real_theory_distribution.svg"))
png.file <- file.path(wddir, paste0(params$sample,".kmer.freq.stat_real_theory_distribution.png"))
library(rsvg)
rsvg_png(svg.file, png.file)