In HIVDiversity/MotifBinner2: Processes NGS Primer ID Datasets

opts_chunk$set(echo=FALSE)
opts_chunk$set(warning=FALSE)
opts_chunk$set(fig.pos = 'H')

library(MotifBinner2)

if (!exists('result'))
{
  result <- all_results[[grep('removeChars', names(all_results))[1]]]
}
if (class(result) != 'removeChars')
{
  result <- all_results[[grep('removeChars', names(all_results))[1]]]
}

r result$config$op_full_name

Removes characters from the sequences.

Characters to remove: r result$config$op_args$char_to_remove

r sum(result$metrics$per_read_metrics$n_gaps > 0) of the sequences contained this character.

On average r mean(result$metrics$per_read_metrics$n_gaps[result$metrics$per_read_metrics$n_gaps > 0]) of the character were removed from a sequence if the sequenced contained at least one of the character.

In total r sum(result$metrics$per_read_metrics$n_gaps[result$metrics$per_read_metrics$n_gaps > 0]) of the character were removed.

kable_summary(result$summary)

timingTable(result)

cat('\n\n---\n\n')

HIVDiversity/MotifBinner2 documentation built on May 6, 2019, 6:44 p.m.