splice_junction_analysis_table: Generate data for splice-junction analysis using multiple...

In vladimirsouza/lrRNAseqBenchmark: Figure out how to call varaints from Iso-Seq data

Generate data for splice-junction analysis using multiple master tables

Description

Generate data to plot variant performance of sites near to and far from splice junctions comparisons using multiple master table as facets.

Usage

splice_junction_analysis_table(
  ...,
  experiment_names,
  truth_names,
  method_dataset_name,
  method_names,
  output_method_names,
  variant_type,
  min_isoseq_coverage
)

Arguments

...	Data.frames. Each data.frame is a master table.
experiment_names	A vector of strings with length equal to the number of master tables input in '...'. Names of the datasets for each data table.
truth_names	A vector of strings. Names of the ground truth in each data table especified in '...'.
method_dataset_name	A vector of strings. Name of the datasets used to call variants, by the methods to be compared, in each input master table.
method_names	A vector of strings. The name of the methods to be compared defined in the input master tables. All master table must have the same 'method_names'.
output_method_names	A vector of strings. The output name of the methods to be compared defined in the input master tables. The output name of the methods will be the same for all master table.
variant_type	A 1-length string. Possible values are "snp" or "indel".
min_isoseq_coverage	A 1-length integer. The threshod value for the minimum Iso-Seq read coverage.

Value

A list of two elements ('acc_sj' and 'n_test') to be used to draw a chart to analyse the variant-calling performance of sites near to and far from splice junctions. 'acc_sj' stores the calculated performance measures, and 'n_test' stores the number of observed variants in each case.

vladimirsouza/lrRNAseqBenchmark documentation built on March 23, 2023, 7:32 a.m.