In xiayh17/RNAseqStat: A Pipeline to Process RNAseq Data

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(RNAseqStat)

DEG analysis

DEG analysis will be run by limma edgeR and DESeq2 in this step.

deg_run(counts_input,group_list,test_group = "T", control_group = "C",dir = results_dir)

Resluts Overview

fl <- list.files("../dev/example_output/")
modules <- fl[grep("2-DEG_DEseq2",fl)]
bitmap_l <- lapply(modules, function(x){
  pdftools::pdf_render_page(glue::glue("../dev/example_output/{x}"), page = 1, dpi = 300)
})
basenames <- gsub(pattern = "\\.pdf$", "", modules)
names(bitmap_l) <- basenames
tmp <- lapply(seq_along(bitmap_l), function(x){
  png::writePNG(bitmap_l[[x]], glue::glue("{names(bitmap_l)[[x]]}.png"))
})

knitr::include_graphics("2-DEG_DEseq2_qc_dispersions.png")

knitr::include_graphics("2-DEG_DEseq2_RAWvsNORM.png")

knitr::include_graphics("2-DEG_DEseq2_top100_heatmap.png")

knitr::include_graphics("2-DEG_DEseq2_volcano.png")

xiayh17/RNAseqStat documentation built on June 16, 2022, 11:51 a.m.