# Noise Quantification in High Throughput Sequencing Output

## Documentation for package ‘noisyr’ version 1.0.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package README

## 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