Render NULISAseq QC HTML Report — render_QC

Generates an HTML quality control report using the NULISAseq R Markdown template skeleton.Rmd.

render_QC_report(
  output_filename,
  output_dir,
  study_name = "NULISAseq QC_Report",
  assayName = NULL,
  dataDir,
  xml_files,
  dataRuns = NULL,
  Rmd_input_file = file.path(system.file(package = "NULISAseqR"),
    "rmarkdown/templates/nulisaseq/skeleton/skeleton.Rmd"),
  plateNames = NULL,
  assayRunInfo = NULL,
  report_type = "internal",
  advancedQC = FALSE,
  IC = NULL,
  IPC = NULL,
  NC = NULL,
  SC = NULL,
  Bridge = NULL,
  rowAnnotName = "AUTO_WELLROW",
  colAnnotName = "AUTO_WELLCOL",
  plateAnnotName = "AUTO_PLATE",
  excludeSamples = NULL,
  excludeTargets = NULL,
  ignoreTargetBlank = NULL,
  minBlankNoMAD = 4,
  plate_effect_pval_ANOVA = 0.01,
  plate_effect_pval_pairwise = 0.01,
  plate_effect_icc_threshold = 10,
  plate_effect_sig_pct_threshold = 10,
  sampleGroupCovar = "SAMPLE_MATRIX",
  outRunSummary = TRUE,
  outPlateLayout = TRUE,
  outReadSummary = TRUE,
  outHeatmaps = TRUE,
  outQC = TRUE,
  outDetectability = TRUE,
  outIntraPlateNorm = TRUE,
  outInterPlateNorm = TRUE,
  outSampleBoxplot = TRUE,
  outSampleCorrelation = TRUE,
  outSampleClustering = TRUE,
  outSamplePCA = TRUE,
  outPlateEffect = TRUE,
  heatMapRel = TRUE,
  outputPlots = TRUE,
  outputDetectCSV = TRUE,
  outputCoefVarCSV = TRUE,
  out_SC_IPC_Ratio = TRUE,
  out_SC_NC_Ratio = TRUE,
  output_SC_IPC_Ratio_CSV = TRUE,
  output_SC_NC_Ratio_CSV = TRUE,
  outputPlateEffectCSV = TRUE,
  outputRData = TRUE,
  rendered_by_shiny = FALSE,
  highlight_TAP_report_fields = TRUE,
  sort_by_plateNames = TRUE,
  ...
)

Arguments

output_filename: Output HTML filename.
output_dir: Output directory for the rendered report.
study_name: Title of the report.
assayName: Name of the assay. Default is NULL.
dataDir: Directory containing XML files.
xml_files: Vector of XML filenames to include.
dataRuns: Optional list of preloaded data objects. Default is NULL.
Rmd_input_file: Path to the R Markdown template file skeleton.Rmd. Defaults to the template in the NULISAseqR package.
plateNames: Optional vector of plate names to override defaults.
assayRunInfo: Optional list of lists with assay run dates and instruments. Default is NULL.
report_type: Type of report: "internal" or "webApp".
advancedQC: Logical; whether to include advanced QC metrics.
IC: Vector of internal control target names to override default behavior.
IPC: Vector of inter-plate control sample identifiers to override default behavior.
NC: Vector of negative control sample identifiers to override default behavior.
SC: Vector of sample control sample identifiers to override default behavior.
Bridge: Vector of bridge sample identifiers to.
rowAnnotName: Column name for row annotation. Default is "AUTO_WELLROW".
colAnnotName: Column name for column annotation. Default is "AUTO_WELLCOL".
plateAnnotName: Column name for plate ID annotations. Default is "AUTO_PLATE".
excludeSamples: List of sample names to exclude per run.
excludeTargets: List of target names to exclude per run.
ignoreTargetBlank: List of named vectors specifying targets and associated blank samples to ignore.
minBlankNoMAD: Minimum number of blanks required for MAD outlier detection. Default is 4.
plate_effect_pval_ANOVA: Unadjusted p-value threshold for ANOVA plate effect detection. Default is 0.01.
plate_effect_pval_pairwise: P-value threshold for pairwise plate effect detection. P-values are Tukey-adjusted. Default is 0.01.
plate_effect_icc_threshold: ICC % threshold for plate effect flagging of targets. Default is 10%.
plate_effect_sig_pct_threshold: Percent threshold of significant targets needed to flag a plate. Default is 10%.
sampleGroupCovar: Column name for sample group variable used in detectability. Default is "SAMPLE_MATRIX".
outRunSummary: Logical. Include Run Summary section. Default is TRUE.
outPlateLayout: Logical. Include Plate Layout section. Default is TRUE.
outReadSummary: Logical. Include Read Summary section. Default is TRUE.
outHeatmaps: Logical. Include Heatmaps. Default is TRUE.
outQC: Logical. Include QC Summary section. Default is TRUE.
outDetectability: Logical. Include Detectability Analysis. Default is TRUE.
outIntraPlateNorm: Logical. Include Intra-Plate CV Analysis. Default is TRUE.
outInterPlateNorm: Logical. Include Inter-Plate CV Analysis. Default is TRUE.
outSampleBoxplot: Logical. Include Sample Boxplots. Default is TRUE.
outSampleCorrelation: Logical. Include Sample Correlation plot. Default is TRUE.
outSampleClustering: Logical. Include Sample Clustering heatmap. Default is TRUE.
outSamplePCA: Logical. Include PCA plot. Default is TRUE.
outPlateEffect: Logical. Include Plate Effect section. Default is TRUE.
heatMapRel: Logical. Whether to use relative (% median) values in heatmaps. Default is TRUE.
outputPlots: Logical. Whether to output slide-friendly plots. Default is TRUE.
outputDetectCSV: Logical. Output CSV of detectability data. Default is TRUE.
outputCoefVarCSV: Logical. Output CSV of coefficient of variation results. Default is TRUE.
out_SC_IPC_Ratio: Logical. Include SC/IPC ratio graphic. Default is TRUE.
out_SC_NC_Ratio: Logical. Include SC/NC ratio graphic. Default is TRUE.
output_SC_IPC_Ratio_CSV: Logical. Output CSV of SC/IPC log2 ratios. Default is TRUE.
output_SC_NC_Ratio_CSV: Logical. Output CSV of SC/NC log2 ratios. Default is TRUE.
outputPlateEffectCSV: Logical. Whether to output plate effect test CSV. Default is TRUE.
outputRData: Logical. Whether to output .RData file of report data. Default is TRUE.
rendered_by_shiny: Logical. Indicates if the report is rendered in a Shiny app. Default is FALSE.
highlight_TAP_report_fields: Logical. Highlight fields required for TAP report. Default is TRUE.
sort_by_plateNames: Logical. Whether to sort runs by plate name. Default is TRUE.
...: Additional named parameters passed to the R Markdown template.

Value

Path to the rendered report (invisible).