02-qc_idats.Rmd

---
params:
  project_name: !r gsub("(.*)_.*", "\\1", list.files(here::here(), pattern = ".Rproj$"))
  title: !r paste0("[", params[["project_name"]], "] EPIC Array Quality-Control")
  author_name: "Mickaël CANOUIL, *Ph.D.*"
  author_affiliation: "INSERM U1283, CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, University of Lille, Lille University Hospital, Lille, F-59000, France."
  author_email: ""
  output_directory: !r here::here("outputs", "02-qc_idats")
  csv_file: !r file.path("/disks/DATA/Projects", params[["project_name"]], "EPIC/sample_sheet.csv")
  design: !r here::here("outputs", "01-design", "design.xlsx")
  data_directory: !r file.path("/disks/DATA/Projects", params[["project_name"]], "EPIC/idats/")
  array: "EPIC"
  annotation: "ilm10b4.hg19"
  filter_snps: TRUE
  filter_non_cpg: TRUE
  filter_xy: TRUE
  filter_multihit: TRUE
  filter_beads: TRUE
  population: NULL
  bead_cutoff: 0.05
  detection_pvalues: 0.01
  filter_callrate: TRUE
  callrate_samples: 0.99
  callrate_probes: 1
  sex_threshold: NULL
  sex_colname: "sexe"
  norm_background: "oob"
  norm_dye: "RELIC"
  norm_quantile: "quantile1"
  cell_tissue: "blood"
  pca: TRUE
  pca_vars: !r c("Sample_Plate", "Sentrix_ID")
  pca_threshold: 2
  max_labels: 15
title: '`r params[["title"]]`'
author:
- name: '`r params[["author_name"]]`'
  affiliation: '`r params[["author_affiliation"]]`'
  email: '`r params[["author_email"]]`'
date: '`r format(Sys.time(), "%B %d, %Y")`'
output:
  bookdown::html_document2:
    theme: simplex
    toc: true
    toc_depth: 3
    toc_float:
      collapsed: false
    fig_width: 6.3
    fig_height: 4.7
    number_sections: true
    self_contained: true
---

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