Creates Plots Showing Sample-Specific Quality Control Metrics

Source: R/sampleQCplot.R

This function generates QC plots for the following metrics:

Detectability

Percentage of targets with reads above the Limit of Detection (LOD). Minimum thresholds vary by sample type.

  • Plasma: 90%

  • Serum: 90%

  • CSF: 70%

  • Urine: 65%

  • Cell culture: 30%

  • NHP plasma: 55%

  • NHP CSF: 35%

  • Dried blood spot: 75%

  • Control: 90%

  • Other: 0%

IC Reads

Number of Internal Control (IC) reads within a sample. Minimum threshold: 1,000 reads

Reads

Total number of reads within a sample. Minimum threshold: 500,000 reads

IC Median

Sample IC reads relative to the plate median. Acceptable range: within +/-40% of plate median

sampleQCplot(
  runs,
  qc_metric = "Detectability",
  plateIDs = NULL,
  output_dir = NULL,
  plot_name = NULL,
  plot_title = NULL,
  plot_width = ifelse(qc_metric == "all", 8, 14),
  plot_height = ifelse(qc_metric == "all", 6, 7),
  label_cex = 0.45,
  point_cex = 0.75,
  legend_cex = 0.75,
  sample_subset_list = NULL,
  target_subset_list = NULL,
  sample_exclude_list = NULL,
  target_exclude_list = NULL
)

Arguments

runs

A named list of run data output from loadNULISAseq() function or a list of these outputs for multiple runs.

qc_metric

The QC metric to plot (default: "Detectability"; select other QC metrics: "IC Reads", "Reads", "IC Median", "all" (showing all 4 metrics)).

plateIDs

Optional vector of plate names. (default: extract from runs).

output_dir

Directory to save PDF files (NULL for no saving).

plot_name

Optional name for the plot file (default: NULL).

plot_title

Optional title for the plot (default: NULL).

plot_width

PDF width in inches (default: 14 for single QC metric plot, 8 for all four QC metric plots).

plot_height

PDF height in inches (default: 7 for single QC metric plot, 6 for all four QC metric plots).

label_cex

Text size for labels (default: 0.45).

point_cex

Point size (default: 0.75).

legend_cex

Legend text size (default: 0.75).

sample_subset_list

Optional list of sample subsets for each plate. Can be either:

  • A list of character vectors - each vector contains sample names to include for the corresponding plate (e.g., `list(c('A_01_C001 P3', 'A_02_C044 P1'), c('A_01_C040 P1'))` for two plates)

  • A single character vector - only subsets samples from the first plate

Note: Control samples (IPC, NC, SC, Bridge) are always included regardless of subsetting. (default: NULL)

target_subset_list

Optional list of target subsets for each plate. Can be either:

  • A list of character vectors - each vector contains target names to include for the corresponding plate

  • A single character vector - only subsets targets from the first plate

(default: NULL)

sample_exclude_list

Optional list of samples to exclude for each plate. Can be either:

  • A list of character vectors - each vector contains sample names to exclude from the corresponding plate

  • A single character vector - only excludes samples from the first plate

Note: Control samples (IPC, NC, SC, Bridge) are never excluded. (default: NULL)

target_exclude_list

Optional list of targets to exclude for each plate. Can be either:

  • A list of character vectors - each vector contains target names to exclude from the corresponding plate

  • A single character vector - only excludes targets from the first plate

(default: NULL)

Value

A list of plot data and saved PDF files in the specified output directory.

Details

For "all" option, plots all four QC metrics in a consolidated view.