README.md

In markheron/pRon: pretty Representations of oligo-nucleotides

pretty Representations of oligo-nucleotides

The pRon package contains functions to help handle oligo-nucleotides (k-mers), including creating frequency/energy profile figures.

Summary

This package provides some useful functions that I frequently used:

• quick summary of large objects in memory
• ruler style axis for plots
• nicer (and more convinient) heatmap
• smearing and running mean functions for fast smoothing

Installation

devtools::install_bitbucket(repo="markheron/pRon", auth_user="user_name", password="your_password")

or install all of Marks packages with the maRs package:

install_marks_package_suite(auth_user="user_name")

Usage

library(pRon)

oligo_names(2)
#>  [1] "AA" "AC" "AG" "AT" "CA" "CC" "CG" "CT" "GA" "GC" "GG" "GT" "TA" "TC"
#> [15] "TG" "TT"

fastas <- cut_out_fasta_multiple(chr=chr_vec, pos = pos_vec, strand = strand_vec, size = 100, order = 2, genome_dir = "path/to/genome")
num_fasta_matrix <- fasta2num(fastas=fastas, oligo_length = 2)
plotOligoFreqs(num_fasta_matrix)

License

The pRon package is licensed under the GPLv3 (http://www.gnu.org/licenses/gpl.html).

markheron/pRon documentation built on Feb. 18, 2020, 12:33 a.m.