negativeQC {NanoTube} | R Documentation

## Calculate negative control statistics

### Description

Provide a table the negative control statistics, and plot the counts of negative control genes in each sample.

### Usage

    negativeQC(ns, interactive.plot = FALSE)

### Arguments

`ns` | NanoString data, processed by 'processNanostringData' with output.format set to 'list' and 'nSolver' normalization.
`interactive.plot` | Generate an interactive plot using plotly? Only recommended for fewer than 20 samples (default FALSE)

### Value

A list object containing:

`tab` | The table of negative control statistics, including the mean & standard deviation of negative control genes, calculated background threshold, and number of endogenous genes below that threshold
`plt` | An object containing the negative control plots.

### Examples

    example_data <- system.file("extdata", "GSE117751_RAW", package = "NanoTube")
    sample_data <- system.file("extdata", "GSE117751_sample_data.csv",
                               package = "NanoTube")

    # Process and normalize data first
    dat <- processNanostringData(example_data,
                                 sampleTab = sample_data,
                                 groupCol = "Sample_Diagnosis",
                                 normalization = "nSolver",
                                 bgType = "threshold",
                                 bgThreshold = 2, bgProportion = 0.5,
                                 output.format = "list")

    negQC <- negativeQC(dat, interactive.plot = FALSE)

    # View negative QC table & plot
    head(negQC$tab)
    negQC$plt

[Package NanoTube version 1.0.0 Index]