simfastq_map_error_repeated: Calculation of error rates with repeated sampling
In Moritz-Kohls/virDisco2: Virus Discovery

Description Usage Arguments Value Examples

This function simulates paired fastq-files, maps these to the reference genomes and calculates mapping and error rates. The whole procedure is repeated multiple times which yields the absolute value and range of the mapping and error rates.

simfastq_map_error_repeated(
  file_indices,
  iterations,
  read_counts,
  start_positions_and_read_lengths,
  seed,
  reference_genome_index_bowtie2.directory,
  mapq_filter_threshold,
  threads
)

`file_indices`	Indices of the mapped sam-files belonging to the simulated paired fastq-files
`iterations`	Number of paired fastq-files to simulate, map and calculate mapping and error rates.
`read_counts`	If the number of reads are "original", the number of reads generated per virus is identical to the read counts of the sam-file. By specifying the parameter as "density", there is the possibility to change the number of reads generated randomly based on a kernel density estimation of the original number of reads mapped to the species. In the latter case, the number of reads of the mapped species which are to be generated differs slightly from the original distribution.
`start_positions_and_read_lengths`	If the start positions and read lengths are "original", the start positions and read lengths are taken from the original sam-files so that every read is used exactly once. In contrary, if the parameter setting is "random", the reads are sampled with replacement so that some reads may be used multiple or zero times.
`seed`	Seed of the random number generator used to simulate paired fastq-files
`reference_genome_index_bowtie2.directory`	# Prefix (folder) of bowtie2 index files
`mapq_filter_threshold`	# Reads with a mapping quality below this threshold will be deleted from the sam-files.
`threads`	Number of threads that are used for mapping

None

library(rChoiceDialogs)
reference_genome_index_bowtie2.directory = rchoose.dir() # Choose prefix (folder) of reference genome bowtie2 index files
my.prefix = gsub("\\\\","/",reference_genome_index_bowtie2.directory)
my.prefix = paste0(my.prefix,"/")
## Not run: simfastq_map_error_repeated ( file_indices = 1 , iterations = 10 , read_counts = "density", start_positions_and_read_lengths = "random" , seed = 42 ,
reference_genome_index_bowtie2.directory = my.prefix , mapq_filter_threshold = 2 , threads = 2 )
## End(Not run)