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

r result$config$op_full_name

r length(result$seq_dat) out of r result$metrics$total_seq reads were sucessfully loaded from file r basename(result$config$op_args$data_source) in the folder r dirname(result$config$op_args$data_source).

If fewer than all the reads were read this is because the max_seq option was specified.

#kable_summary(result$summary)

summary_tab <- result$summary
cat('\n\nTable: Basic statistics of the loaded sequences.\n\n')
kept_tab <- summary_tab[,grep('k_', names(summary_tab))]
names(kept_tab) <- gsub('k_', '', names(kept_tab))
print(format_table(kept_tab))

timingTable(result)

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

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