noisyr_counts_with_plot {bulkAnalyseR} | R Documentation |
Apply a modified noisyR counts pipeline printing a plot
Description
This function is identical to the noisyr::noisyr_counts function, with the addition of the option to print a line plot of the similarity against expression for all samples.
Usage
noisyr_counts_with_plot(
expression.matrix,
n.elements.per.window = NULL,
optimise.window.length.logical = FALSE,
similarity.threshold = 0.25,
method.chosen = "Boxplot-IQR",
...,
output.plot = FALSE
)
Arguments
expression.matrix |
the expression matrix; rows correspond to genes and columns correspond to samples |
n.elements.per.window |
number of elements to have in a window passed to calculate_expression_similarity_counts(); default 10% of the number of rows |
optimise.window.length.logical |
whether to call optimise_window_length to try and optimise the value of n.elements.per.window |
similarity.threshold , method.chosen |
parameters passed on to
|
... |
optional arguments passed on to |
output.plot |
whether to create an expression-similarity plot for the noise analysis (printed to the console); default is FALSE |
Value
The denoised expression matrix.
Examples
expression.matrix <- as.matrix(read.csv(
system.file("extdata", "expression_matrix.csv", package = "bulkAnalyseR"),
row.names = 1
))[1:10, 1:4]
expression.matrix.denoised <- noisyr_counts_with_plot(expression.matrix)