assessHousekeeping,RccSet-method {NanoStringQCPro} | R Documentation |
Assess correlation and variance/variability of housekeeping genes
## S4 method for signature 'RccSet' assessHousekeeping(rccSet, hk, covar, annotate = TRUE, plot = TRUE, digits = 2)
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 |
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.
A dataframe with one row per housekeeping genes and several columns with metrics suggested to assess performance of defined housekeeping genes.
Dorothee Nickles