qc_median_intensities function

Median run intensities

Median intensities per run are returned either as a plot or a table.

qc_median_intensities(
  data,
  sample,
  grouping,
  intensity,
  plot = TRUE,
  interactive = FALSE
)

Arguments

• data: a data frame that contains at least the input variables.
• sample: a character or factor column in the data data frame that contains the sample name.
• grouping: a character column in the data data frame that contains either precursor or peptide identifiers.
• intensity: a numeric column in the data data frame that contains intensity values. The intensity should be ideally log2 transformed, but also non-transformed values can be used.
• plot: a logical value that indicates whether the result should be plotted.
• interactive: a logical value that specifies whether the plot should be interactive (default is FALSE).

Returns

A plot that displays median intensity over all samples. If plot = FALSE a data frame containing median intensities is returned.

Examples

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"
)

# Calculate median intensities
qc_median_intensities(
  data = data,
  sample = sample,
  grouping = peptide,
  intensity = peptide_intensity_missing,
  plot = FALSE
)

# Plot median intensities
qc_median_intensities(
  data = data,
  sample = sample,
  grouping = peptide,
  intensity = peptide_intensity_missing,
  plot = TRUE
)