assessHousekeeping: assessHousekeeping

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

Description

Assess correlation and variance/variability of housekeeping genes

Usage

## S4 method for signature 'RccSet'
assessHousekeeping(rccSet, hk, covar, annotate = TRUE,
  plot = TRUE, digits = 2)

Arguments

rccSet	An RccSet object
hk	Either a boolean vector of length nrow(exprs(rccSet)) or a numeric vector of indices which genes in exprs(rccSet) are housekeeping genes
covar	character; colname in fData(rccSet) that can be used to label genes by a category of interest
annotate	Scalar boolean; if TRUE (default), probes will be "annotated" using the "GeneName" column in the fData(rccSet) slot
plot	Scalar boolean, plot pairwise relationships ?
digits	Scalar integer, the number of decimal places

Details

Pairwise correlations of all defined housekeeping genes will be assessed and pairwise scatterplots will be generated. This function does not only output pairwise correlation coefficients, but also - for each housekeeping gene - the variance, the interquartile range (IQR) and median expression level across all samples in the experiment.

Value

A dataframe with one row per housekeeping genes and several columns with metrics suggested to assess performance of defined housekeeping genes.

Author(s)

Dorothee Nickles

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