negativeQC {NanoTube} | R Documentation |
Provide a table the negative control statistics, and plot the counts of negative control genes in each sample.
negativeQC(ns, interactive.plot = FALSE)
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) |
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. |
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