🎯 Ntermreport R Package — Reports for N-terminal and LFQ Experiments Welcome to Ntermreport — your ultimate companion for comprehensive reports on DDA enriched N-terminal experiments and non-enriched LFQ proteomics experiments. 🧑‍🔬🔬

With Ntermreport, you can generate in-depth analysis reports for both N-terminal–enriched datasets and standard LFQ workflows with just one magical command. ✨

🛠️ Requirements Installation

1. Install R version >= 4.4.0

2. Install Bioconductor: install.packages("BiocManager")

3. Install PhantomJS: webshot::install_phantomjs()

4. Install devtools: install.packages("devtools")

5. Install Quarto:

   Follow the instructions on the Quarto website.

6. Install diareport devtools::install_github('Gevaert-Lab/diareport')

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🛠 How to Install the R Package

For development use:

1. Clone the GitHub repository.

2. Use devtools::install() to install the diareport package on your system.

To test the R package:

devtools::install_github('Gevaert-Lab/ntermreport')

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📂 Analysis Templates Available

The repository contains Quarto templates, for different analysis:

• id_report: Identification Analysys from Mascot PSM and petide result
• quant_report : Quantitification Analysis from Mascot petide files (not yet available)

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🚀 How to Run an Analysis

The three main functions to render HTML reports are:

• render_nterm_report

  It renders an HTML report for the N-terminal–enriched DDA analysis, starting from the Mascot PSM file.

List of the input parameters:

Pameter	Description
input_file	Full path to the PSM results file (e.g., PSM, peptide, or protein table) generated from the N-terminal enriched DDA experiment. The peptide file must be located in the folder
design_file	Full path to the experimental design CSV file, containing sample names, conditions, and grouping information.
folder_prj	Path to the folder where the report output and intermediate results will be saved.
description	Short text describing the experiment’s purpose or biological context.
title	Main title for the report.
subtitle	Secondary title, often used to indicate experiment type (e.g., “N-Terminal”).
author	Name(s) of the report author(s), shown in the report header.
select_group	A list of group names to include in the comparison. It must contain at least one element, and each element must be a valid name from the experimental design column Group. Example: list(Comparison = c("GrpA", "GrpB"))

Function parameters:

Pameter	Description
params	a list of parameters described above
template	Name of the Quarto template file used to generate the report (e.g., Template_DDA.qmd).
report_folder	Folder where the final report will be stored (usually the same as folder_prj).
report_filename	Name of the output report file without the file extention (e.g., test).

Example:

report_target_folder  <- 'C:\\path\\to\\your\\data\\N-term\\AnalysisFolder'
template_file = c('id_report')
output_filename = "test"

params <- list(
  input_file  = 'C:\\path\\to\\your\\data\\N-term\\Nterminal_output_PSM.tsv',
  design_file = 'C:\\path\\to\\your\\data\\N-term\\exp_design_dda_2groups.csv',
  folder_prj  = report_target_folder, 
  description = 'N-terminal enrichment on retina samples',
  title       = 'CMB - XXYY',
  subtitle    = "N-Terminal",
  author      = 'Your Name',
  select_group= list(Comparison = c("GrpA", "GrpB"))
)

# To run the analysis:
render_nterm_report(
  params,
  template       = template_file,
  report_folder  = report_target_folder,
  report_filename = output_filename
)

• render_nterm_website

!! !! Not yet refactored TO DO

This function renders both DDA and DIA reports in a small website created by Quarto and accepts the following parameters:

Parameter	Description
params_dda	A named list of parameters passed to the N-terminal enriched DDA report rendering function. Defines input files, metadata, and analysis settings for the DDA workflow. See the parameters described above
params_dia	A named list of parameters passed to the DIA report rendering function. Defines input files, metadata, and analysis settings for the DIA workflow.
template_dda	Full path to the Quarto template (.qmd) used to generate the N-terminal enriched DDA report.
report_folder	Directory where the final rendered website/report will be saved. Must be writable and preferably empty before rendering.
template_dia	Full path to the Quarto template (.qmd) used to generate the DIA report.

Example:

# Output folder for the reports
report_folder  <- 'C:\\path\\to\\project\\Nterm_all'

# DIA parameters and template
template_dia <- "Template_DIA-NN_dev_A.qmd"

params_dia <- list(
  title        = "Project XYZ N-terminal DIA LFQ",
  subtitle     = "DE Analysis",
  author       = "Author Name",
  description  = "Retina Samples",
  input_file   = 'C:\\path\\to\\data\\nterm_lfq\\report.parquet',
  design_file  = 'C:\\path\\to\\data\\nterm_lfq\\exp_design_dia_2groups.csv',
  folder_prj   = report_folder,
  contrast     = 'Group',
  aggr_method  = 'medianPolish',
  normalization = 'center.median',
  formula      = '~ -1 + Group',
  confounder_list = '',
  PCA_comparison  = c('Group'),
  Proteotypic     = TRUE,
  pep_per_prot    = 2,
  nNonZero        = 50,
  FC_thr          = 2,
  comparisons     = c('GroupNR - GroupRPE'),
  filtPerGroup    = 'at_least_one',
  wildstr_run     = 'Project-',
  mbr             = TRUE,
  DIANN_ver2      = TRUE,
  comparison_label = c('NR - RPE'),
  filtering_contaminant = TRUE,
  contaminant_str = 'cRAP-',
  filt_NaNDE      = TRUE
)

# DDA parameters and template
template_dda <- "Template_DDA.qmd"

params_dda <- list(
  input_file  = 'C:\\path\\to\\data\\nterm_dda\\Nterminal_output_PSM.tsv',
  design_file = 'C:\\path\\to\\data\\nterm_dda\\exp_design_dda_2groups.csv',
  folder_prj  = report_folder,
  description = 'N-terminal enrichment on retina samples',
  title       = 'Project - ABCD',
  subtitle    = "N-Terminal",
  author      = 'Author Name',
  select_group = list(Comparison = c("GrpA", "GrpB"))
)
render_nterm_website ( params_dda , params_dia , template_dda, report_folder, template_dia , 'CMB-1699 CMB-XXXX' )

• render_ntermdia_report

  This function is a simple wrapper for the diareport::render_dia_report function. See the documentation for more information about the parameters and how to use it.

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📝 Experiment Design File (EDF)

The experiment design file is a CSV that must include the following columns:

• Sample: Sample name (used in all plots, should be meaningful and not too long)
• Run: Raw file name without file extension (mzML/.d/.raw)
• Group: Groups in the experiment (e.g., Cancer/control, mutation/WT)
• Replicate: Label for the sample replicates

Example:

Sample	Run	Group	Replicate
B000250_ratio01_DIA	B000250_Ap_6883_EXT-765_DIA_Yeast_UPS2_ratio01_DIA	A	1
B000254_ratio02_DIA	B000254_Ap_6883_EXT-765_DIA_Yeast_UPS2_ratio02_DIA	B	1
B000258_ratio04_DIA	B000258_Ap_6883_EXT-765_DIA_Yeast_UPS2_ratio04_DIA	C	1
B000262_ratio08_DIA	B000262_Ap_6883_EXT-765_DIA_Yeast_UPS2_ratio08_DIA	D	1
B000266_ratio10_DIA	B000266_Ap_6883_EXT-765_DIA_Yeast_UPS2_ratio10_DIA	E	1