inst/doc/quality_control_workflow.R

In protti: Bottom-Up Proteomics and LiP-MS Quality Control and Data Analysis Tools

## ----include = FALSE----------------------------------------------------------
test_protti <- identical(Sys.getenv("TEST_PROTTI"), "true")
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## ----setup, eval = test_protti, message = FALSE, warning = FALSE--------------
# library(protti)
# library(magrittr)
# library(dplyr)

## ----create_synthetic_data, eval = test_protti--------------------------------
# # by setting the seed we are making sure that the random object generation can be reproduced
# set.seed(123)
# 
# data <- create_synthetic_data(
#   n_proteins = 100,
#   frac_change = 0.05,
#   n_replicates = 3,
#   n_conditions = 2,
#   method = "effect_random",
#   additional_metadata = TRUE
# )

## ----qc_cvs, eval = test_protti, fig.width = 6, fig.height = 4, fig.align = "center"----
# input <- data %>%
#   # as the data is log2 transformed, we need to transform it back before calculating the CVs
#   mutate(raw_intensity = 2^peptide_intensity_missing)
# 
# qc_cvs(
#   data = input,
#   grouping = peptide,
#   condition = condition,
#   intensity = raw_intensity,
#   plot = FALSE
# )
# 
# qc_cvs(
#   data = input,
#   grouping = peptide,
#   condition = condition,
#   intensity = raw_intensity,
#   plot = TRUE,
#   plot_style = "violin"
# )

## ----qc_ids, eval = test_protti, fig.width = 6, fig.height = 4, fig.align = "center"----
# qc_ids(
#   data = input,
#   sample = sample,
#   grouping = protein,
#   intensity = peptide_intensity_missing,
#   condition = condition,
#   plot = FALSE
# )
# 
# qc_ids(
#   data = input,
#   sample = sample,
#   grouping = protein,
#   intensity = peptide_intensity_missing,
#   condition = condition,
#   title = "Protein identifications per sample",
#   plot = TRUE
# )

## ----qc_peptide_type, eval = test_protti, fig.width = 6, fig.height = 4, fig.align = "center"----
# qc_peptide_type(
#   data = input,
#   sample = sample,
#   peptide = peptide,
#   pep_type = pep_type,
#   method = "intensity",
#   intensity = raw_intensity,
#   plot = TRUE,
#   interactive = FALSE
# )
# 
# qc_peptide_type(
#   data = input,
#   sample = sample,
#   peptide = peptide,
#   pep_type = pep_type,
#   method = "count",
#   plot = TRUE,
#   interactive = FALSE
# )

## ----qc_intensity_distribution_boxplot, eval = test_protti, fig.width = 6, fig.height = 4, fig.align = "center"----
# qc_intensity_distribution(
#   data = input,
#   sample = sample,
#   grouping = peptide,
#   intensity_log2 = peptide_intensity_missing,
#   plot_style = "boxplot"
# )
# 
# qc_median_intensities(
#   data = input,
#   sample = sample,
#   grouping = peptide,
#   intensity = peptide_intensity_missing
# )

## ----qc_charge_states, eval = test_protti, fig.width = 6, fig.height = 4, fig.align = "center"----
# qc_charge_states(
#   data = input,
#   sample = sample,
#   grouping = peptide,
#   charge_states = charge,
#   method = "intensity",
#   intensity = raw_intensity,
#   plot = TRUE
# )

## ----qc_missed_cleavages, eval = test_protti, fig.width = 6, fig.height = 4, fig.align = "center"----
# qc_missed_cleavages(
#   data = input,
#   sample = sample,
#   grouping = peptide,
#   missed_cleavages = n_missed_cleavage,
#   method = "intensity",
#   intensity = raw_intensity,
#   plot = TRUE
# )

## ----qc_sequence_coverage, eval = test_protti, fig.width = 6, fig.height = 4, fig.align = "center"----
# qc_sequence_coverage(
#   data = input,
#   protein_identifier = protein,
#   coverage = coverage
# )

## ----qc_peak_width, eval = test_protti, fig.width = 6, fig.height = 4, fig.align = "center"----
# qc_peak_width(
#   data = input,
#   sample = sample,
#   intensity = peptide_intensity_missing,
#   retention_time = retention_time,
#   peak_width = peak_width
# )

## ----qc_data_completeness, eval = test_protti, fig.width = 6, fig.height = 4, fig.align = "center"----
# qc_data_completeness(
#   data = input,
#   sample = sample,
#   grouping = peptide,
#   intensity = peptide_intensity_missing,
#   plot = TRUE
# )

## ----qc_intensity_distribution_histogram, eval = test_protti, fig.width = 6, fig.height = 4, fig.align = "center"----
# qc_intensity_distribution(
#   data = input,
#   grouping = peptide,
#   intensity_log2 = peptide_intensity_missing,
#   plot_style = "histogram"
# )

## ----qc_sample_correlation, eval = test_protti, fig.width = 6, fig.height = 4, fig.align = "center"----
# qc_sample_correlation(
#   data = input,
#   sample = sample,
#   grouping = peptide,
#   intensity_log2 = peptide_intensity_missing,
#   condition = condition,
#   interactive = FALSE
# )

## ----qc_pca, eval = test_protti, fig.width = 6, fig.height = 4, fig.align = "center"----
# qc_pca(
#   data = data,
#   sample = sample,
#   grouping = peptide,
#   intensity = peptide_intensity_missing,
#   condition = condition,
#   digestion = NULL,
#   plot_style = "scree"
# )
# 
# qc_pca(
#   data = data,
#   sample = sample,
#   grouping = peptide,
#   intensity = peptide_intensity_missing,
#   condition = condition,
#   components = c("PC1", "PC2"),
#   plot_style = "pca"
# )

## ----qc_ranked_intensities, eval = test_protti, fig.width = 6, fig.height = 4, fig.align = "center"----
# # Plot ranked peptide intensities
# qc_ranked_intensities(
#   data = data,
#   sample = sample,
#   grouping = peptide,
#   intensity_log2 = peptide_intensity,
#   plot = TRUE,
# )