contentNorm: Content normalization

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

Description

Performs content normalization on the given RccSet.

Usage

## S4 method for signature 'RccSet'
contentNorm(rccSet, method = c("global", "housekeeping"),
  summaryFunction = "median", hk = NULL, inputMatrix = c("bgCorrData",
  "posCtrlData", "exprs"), quietly = FALSE)

Arguments

rccSet	An RccSet.
method	Specifies the features to be used for 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.
summaryFunction	Character specifying the summary function to apply to the selected features (e.g. "mean" or "median"). User-defined functions similar to these can be specified here as well.
hk	Logical vector defining, for each feature, whether or not it shall be used for housekeeping normalization if housekeeping is specified as the normalization method.
inputMatrix	Name of the matrix in the RccSet's assayData to use as input for performing content normalization (one of "exprs", "posCtrlData", or "bgCorrData"). If posCtrlData or bgCorrData are specified but not found in the assayData, an error will be generated.
quietly	Boolean specifying whether or not messages and warnings should be omitted.

Value

A copy of the input is returned with a new matrix named ‘normData’ added to the assayData that contains the content-normalized counts. (NOTE: normData contains values on a log2 scale while all other matrices in assayData are on a linear scale.) If housekeeping is specified as the normalization method, then the housekeeping features used will be recorded in the returned RccSet in a new featureData column named ‘Housekeeping’. Parameters specified in the function call are also recorded in the output's experimentData@preprocessing list.

Author(s)

Dorothee Nickles

Examples

data(example_rccSet)

pcnorm_example_rccSet <- posCtrlNorm(example_rccSet)
bg <- getBackground(pcnorm_example_rccSet)
bgcorr_example_rccSet <- subtractBackground(pcnorm_example_rccSet, bg)

gmnorm_example_rccSet <- contentNorm(bgcorr_example_rccSet, method="global",
    inputMatrix="exprs")
hknorm_example_rccSet <- contentNorm(bgcorr_example_rccSet, method="housekeeping",
    summaryFunction="mean")

NanoStringQCPro documentation built on Nov. 8, 2020, 8:11 p.m.