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 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).

Value

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 )
#> # A tibble: 6 × 2 #> sample median_intensity #> <chr> <dbl> #> 1 sample_1 17.3 #> 2 sample_2 17.3 #> 3 sample_3 17.4 #> 4 sample_4 17.4 #> 5 sample_5 17.4 #> 6 sample_6 17.4
# Plot median intensities qc_median_intensities( data = data, sample = sample, grouping = peptide, intensity = peptide_intensity_missing, plot = TRUE )