make_homopolymer_table_to_plot: Organize the data used to make plots about homopolymer...

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

Organize the data used to make plots about homopolymer analysis

Description

The user may want to use this function several times to pull information about different combinations between 'variant_type' and 'method_name' from 'input_hom_table'. In the future, the function should make the job automatically using loops.

Usage

make_homopolymer_table_to_plot(
  input_hom_table,
  variant_type,
  method_name,
  truth_name,
  hom_length_intervals,
  interval_names,
  to_calculate,
  output_method_name
)

Arguments

input_hom_table	A data.frame generated by function 'method_homopolymer_indels'.
variant_type	A 1-length string. Possible values are "insertion" or "deletion".
method_name	A 1-length string. The name of the method from which is desired to extract information.
truth_name	A 1-length string. The name of the ground-truth.
hom_length_intervals	A vector of integers. The minimum for each interval of homopolymer length. Each interval 'i' ranges from 'hom_length_intervals[i]' to 'hom_length_intervals[i+1]', except the last interval which upper limit is 'Inf'.
interval_names	A vector of characters with the same length of 'hom_length_intervals'. The name for each interval of homopolymer length.
to_calculate	A 1-length string. Possible values are "rates" or "pre_rec_f1". If "rates", the functin calculates the rates of TPs, FNs and FPs. If "pre_rec_f1", it calculates the precision, the recall and the F1-score.
output_method_name	A 1-length string. The label of the method specified in 'method_name' to be output.

Value

A 2-length list ('class_counts' and 'dat_text').

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