NanoStringQCPro: Quality metrics and data processing methods for NanoString mRNA gene expression dat

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## S4 method for signature 'RccSet'
preprocRccSet(rccSet, doPosCtrlNorm = TRUE,
  doBackground = TRUE, doPresAbs = TRUE, doContentNorm = TRUE,
  pcnSummaryFunction = "sum", bgReference = c("both", "blanks",
  "negatives"), bgSummaryFunction = "median", bgStringency = 1,
  nSolverBackground.w1 = 2.18, nSolverBackground.shrink = TRUE,
  paStringency = 2, normMethod = c("global", "housekeeping"),
  normSummaryFunction = "median", hkgenes = NULL, hkfeatures = NULL,
  quietly = FALSE)
  

An RccSet.

Boolean specifying whether or not to perform positive control normalization. (‘pcd’ is short for ‘posCtrlData’, the matrix which gets added to assayData when this step is performed.)

Boolean specifying whether or not to perform background correction.

Boolean specifying whether or not the presence/absence call should be performed. For details, see presAbsCall().

Boolean specifying whether or not content normalization should be performed.

Function to be used for the positive control normalization (e.g. "mean", "median", or "sum"). User-defined functions similar to these can be specified here as well.

Measurements to use for background estimates: either "blank" (for blank samples), "negatives" (for negative control probes), or "both". For details on exactly how the background estimates are computed in each case, see getBackground().

Summary function for background measurements (e.g. "mean" or "median"). User-defined functions similar to these can be specified here as well.

Factor by which deviation (SD or MAD) of the summarization output will be multiplied to obtain final background estimates.

Value to use for the 'w1' argument to nSolverBackground(). (Only takes effect if bgReference == "both"; see getBackground().)

Value to use for the 'shrink' argument to nSolverBackground(). (Only takes effect if bgReference == "both"; see getBackground().)

Multiplier to use in establishing the presence/absence call. For details, see presAbsCall().

Specifies the features to be used for content normalization. "global" indicates that all features should be used and "housekeeping" indicates that only housekeeping features should be used. If "housekeeping" is specified and the ‘hk’ argument (below) is also specified, then the features indicated by ‘hk’ will be used. If "housekeeping" is specified and ‘hk’ is left NULL, then the default housekeeping features (i.e. those with CodeClass == "Housekeeping") will be used.

Character specifying the summary function to apply to the selected features (e.g. "mean" or "median") during the content normalization step. User-defined functions similar to these can be specified here as well.

Character vector with gene symbols to be used for content normalization if housekeeping is specified as the normalization method. If specified, all features that match any of the specified symbols will be used. (To specify specific features, use the ‘hkfeatures’ argument instead; see below.)

Character vector with full feature names ("<CodeClass>_<GeneName>_<Accession>", e.g. "Endogenous_ACTG1_NM_001614.1") to be used for content normalization if housekeeping is specified as the normalization method. (Note: if this argument is specified at the same time as ‘hkgenes’, an error will be thrown.)

Boolean specifying whether or not messages and warnings should be omitted.