Noise Quantification in High Throughput Sequencing Output

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Documentation for package ‘noisyr’ version 1.0.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

calculate_expression_profile	Calculate the expression profile of a gene
calculate_expression_similarity_counts	Calcualate the expression levels and expression levels similarity matrices using the count matrix
calculate_expression_similarity_transcript	Calcualte the distance matrices using the BAM files
calculate_first_minimum_density	Function to find the first local minimum of the density of a vector
calculate_noise_threshold	Function to calculate the noise threshold for a given expression matrix and parameters
calculate_noise_threshold_method_statistics	Function to tabulate statistics for different methods of calculating the noise threshold
cast_gtf_to_genes	Function to extract exon names and positions from a gtf file
cast_matrix_to_numeric	Cast a matrix of any type to numeric
filter_genes_transcript	Function to filter the gene table for the transcript approach
get_methods_calculate_noise_threshold	Show the methods for calculating a noise threshold
get_methods_correlation_distance	Show the methods for calculating correlation or distance
noisyr	Run the noisyR pipeline
noisyr_counts	Run the noisyR pipeline for the count matrix approach
noisyr_transcript	Run the noisyR pipeline for the transcript approach
optimise_window_length	Optimise the elements per window for the count matrix approach
plot_expression_similarity	Plot the similarity against expression levels
remove_noise_from_bams	Function to remove the noisy reads from the BAM files
remove_noise_from_matrix	Function to remove the noisy reads from the expression matrix