preprocessExpressionMatrix: Pre-process the expression matrix before generating the shiny...

In bulkAnalyseR: Interactive Shiny App for Bulk Sequencing Data

Pre-process the expression matrix before generating the shiny app

Description

This function denoises the expression matrix using the noisyR package and then normalises it. It is recommended to use this function before using generateShinyApp.

Usage

preprocessExpressionMatrix(
  expression.matrix,
  denoise = TRUE,
  output.plot = FALSE,
  normalisation.method = c("quantile", "rpm", "tmm", "deseq2", "median"),
  n_million = 1,
  ...
)

Arguments

expression.matrix	the expression matrix; rows correspond to genes and columns correspond to samples
denoise	whether to use noisyR to denoise the expression matrix; proceeding without denoising data is not recommended
output.plot	whether to create an expression-similarity plot for the noise analysis (printed to the console); default is FALSE
normalisation.method	the normalisation method to be used; default is quantile; any unrecognised input will result in no normalisation being applied, but proceeding with un-normalised data is not recommended; currently supported normalisation methods are: quantile Quantile normalisation using the normalize.quantiles function from the preprocessCore package rpm RPM (reads per million) normalisation, where each sample is scaled by 1 (or more using the n_million parameter) million and divided by the total number of reads in that sample tmm Trimmed Mean of M values normalisation using the calcNormFactors function from the edgeR package deseq2 Size factor normalisation using the estimateSizeFactorsForMatrix function from the DESeq2 package median Normalisation using the median, where each sample is scaled by the median expression in the sample divided by the total number of reads in that sample
n_million	scaling factor for RPM normalisation; default is 1 million
...	optional arguments passed on to noisyr::noisyr_counts()

Value

The denoised, normalised expression matrix; some rows (genes) may have been removed by noisyR.

Examples

expression.matrix <- as.matrix(read.csv(
  system.file("extdata", "expression_matrix.csv", package = "bulkAnalyseR"), 
  row.names = 1
))[1:10, 1:4]
expression.matrix.preproc <- preprocessExpressionMatrix(expression.matrix)

bulkAnalyseR documentation built on Dec. 28, 2022, 2:04 a.m.