protti (version 0.9.0)

qc_cvs: Check CV distribution

Description

Calculates and plots the coefficients of variation for the selected grouping.

Usage

qc_cvs(
  data,
  grouping,
  condition,
  intensity,
  plot = TRUE,
  plot_style = "density",
  max_cv = 200
)

Value

Either a data frame with the median CVs in % or a plot showing the distribution of the CVs is returned.

Arguments

data

a data frame containing at least peptide, precursor or protein identifiers, information on conditions and intensity values for each peptide, precursor or protein.

grouping

a character column in the data data frame that contains the grouping variables (e.g. peptides, precursors or proteins).

condition

a character or factor column in the data data frame that contains condition information (e.g. "treated" and "control").

intensity

a numeric column in the data data frame that contains the corresponding raw or untransformed normalised intensity values for each peptide or precursor.

plot

a logical value that indicates whether the result should be plotted.

plot_style

a character value that indicates the plotting style. plot_style = "boxplot" plots a boxplot, whereas plot_style = "density" plots the CV density distribution. plot_style = "violin" returns a violin plot. Default is plot_style = "density".

max_cv

a numeric value that specifies the maximum percentage of CVs that should be included in the returned plot. The default value is max_cv = 200.

Examples

# Load libraries
library(dplyr)

set.seed(123) # Makes example reproducible

# Create example data
data <- create_synthetic_data(
  n_proteins = 100,
  frac_change = 0.05,
  n_replicates = 3,
  n_conditions = 2,
  method = "effect_random"
) %>%
  mutate(intensity_non_log2 = 2^peptide_intensity_missing)

# Calculate coefficients of variation
qc_cvs(
  data = data,
  grouping = peptide,
  condition = condition,
  intensity = intensity_non_log2,
  plot = FALSE
)

# Plot coefficients of variation
# Different plot styles are available
qc_cvs(
  data = data,
  grouping = peptide,
  condition = condition,
  intensity = intensity_non_log2,
  plot = TRUE,
  plot_style = "violin"
)