remove_noise_from_matrix: Function to remove the noisy reads from the expression matrix

In noisyr: Noise Quantification in High Throughput Sequencing Output

Description

This function is used to remove the noisy reads from the expression matrix. It uses as input a vector of abundance thresholds; all entries below the noise threshold are replaced with the noise threshold.

Usage

remove_noise_from_matrix(
  expression.matrix,
  noise.thresholds,
  add.threshold = TRUE,
  average.threshold = TRUE,
  remove.noisy.features = TRUE,
  export.csv = NULL,
  ...
)

Arguments

expression.matrix	the expression matrix
noise.thresholds	a vector of expression thresholds by sample; must be the same length as the number of columns of the expression matrix, or a singular value to be used as a fixed noise threshold
add.threshold	whether to add the noise threshold to all values in the expression matrix (default), or set entries below the threshold to the threshold
average.threshold	if TRUE (default), uses tthe average of the vector of thresholds across all samples; if FALSE, uses the thresholds as supplied
remove.noisy.features	logical, whether rows of the expression matrix that are fully under the noise threshold should be removed (default TRUE)
export.csv	option to write the matrix into a csv after the noise removal; should be NULL or the name of the output file
...	arguments passed on to other methods

Value

Returns the expression matrix with the noise removed. Under default parameters, the denoised matrix will have fewer rows than the input matrix and will have no entries remaining below the noise threshold.

See Also

remove_noise_from_bams

Examples

expression.matrix <- matrix(1:100, ncol=5)
noise.thresholds <- c(5,30,45,62,83)
remove_noise_from_matrix(
    expression.matrix = expression.matrix,
    noise.thresholds = noise.thresholds
)

noisyr documentation built on April 16, 2021, 5:07 p.m.