This function processes codon usage data generated by
per nucleotide position (i.e. positional codon usage) as well as
summed up over all positions* (i.e. bulk codon usage)
for a specific data type, originating compartment, and read length, as well as based on a user-defined genetic code.
This data is used as input in
to generate a bar plot, and in
plot_codon_usage_bulk_rmd to iterativly generate plots for the Ribo-seQC report in section 7.2.
plot_codon_usage for positional codon usage (instead of bulk codon usage).
* Information on positions included in analysis:
Based on P-site corrected reads, the codon usage within CDS regions for protein coding genes is examplatory calculated
for the first 11 codons of the CDS (referred to as start),
for 11 codons from the middle of the CDS (referred to as middle), and
for the last 11 codons of the CDS (referred to as stop).
Object (list of lists) generated by
String; select one of the following:
String for originating compartment.
String for read length.
This function returns a list (e.g. called codon_usage_bulk_data) with information on bulk codon usage:
codon_usage_bulk_data$data contains the data on bulk codon usage,
codon_usage_bulk_data$data_type saves the data type used (see parameter
codon_usage_bulk_data$comp saves the originating compartment used (see parameter
codon_usage_bulk_data$rl saves the read length used (see parameter
Dominique Sydow, [email protected]
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