In bigbio/PepBed: The PepBedR is an R-package to analyze peptide based Bed and bigBed files.

knitr::opts_chunk$set(echo = TRUE)

# define all requiered variables
peptide_counts_table <- counts
unique_peptide_counts_table <- counts_unique
coverage_table <- coverage
coverage_barplot <- plot
circos_plot_path <- temporal_file

Summary of peptide counts per chromosome.

\footnotesize

  pander::pandoc.table(peptide_counts_table, digits = 4,  split.table = Inf,
                       caption = 'Number of peptides per chromosome.')

\newpage

Summary of unique peptide counts per chromosome.

  pander::pandoc.table(unique_peptide_counts_table, digits = 4,  split.table = Inf,
                       caption = 'Number of unique peptides per chromosome.')

\newpage

Summary of coverage percentage per chromosome.

  pander::pandoc.table(coverage_table, digits = 4,  split.table = Inf,
                       caption = 'Coverage (%) at transcript level.')

\newpage

Plots

Transcript coverage percentage per chromosome

   coverage_barplot

\newpage

knitr::include_graphics(path = circos_plot_path)

bigbio/PepBed documentation built on May 28, 2019, 7:11 p.m.