negativeQC: Calculate negative control statistics
In calebclass/NanoTube: An Easy Pipeline for NanoString nCounter Data Analysis

negativeQC

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

calebclass/NanoTube documentation built on Nov. 21, 2023, 12:31 p.m.