flagSamplesCount: flagSamplesCount

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

Description

Flag samples based on overall counts

Usage

## S4 method for signature 'RccSet'
flagSamplesCount(rccSet, method = c("cutoffByMMAD",
  "cutoffByVar"), stringency = 4, maxMiss = 0.2)

Arguments

rccSet	An RccSet object
method	Character string specifying the method for outlier detection: either "cutoffByMMAD" or "cutoffByVar".
stringency	Numeric value passed to the cutoff function specified by the method argument (see the 'd' argument of cutoffByMMAD and cutoffByVar).
maxMiss	Numeric specifying the allowable fraction of genes below the lower limit of detection in a sample.

Details

The method and stringency arguments deterine a cutoff value used to flag samples as outliers: samples will be flagged if the sum of counts of their endogeneous genes exceeds the cutoff or if the ratio of the sums of their positive controls to the sums of their endogenous genes exceeds three times the cutoff. Samples will also be flagged if the fraction of genes below the lower limit of detection exceeds the maxMiss value.

Value

A numeric vector giving the indices of samples with outlier values according to the criteria described above.

Author(s)

Dorothee Nickles

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