In xiayh17/RNAseqStat: A Pipeline to Process RNAseq Data

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

library(RNAseqStat)

Check your data

This step is useful to quickly check you data. dir Can be any wherr you want to save results file.

pre_check(counts_data = counts_input, group_list = group_list, dir = results_dir)

Resluts Overview

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

knitr::include_graphics("1-pre_check_cor_all.png")

knitr::include_graphics("1-pre_check_cor_top500.png")

knitr::include_graphics("1-pre_check_heatmap_top1000_sd.png")

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