vignettes/Statistics.R

In HajkD/seqstats: A Statistical Analysis Package for Biological Sequences

## ---- echo = FALSE, message = FALSE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
library(seqstats)
options(width = 750)
knitr::opts_chunk$set(
  comment = "#>",
  error = FALSE,
  tidy = FALSE)

## ----eval=FALSE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
#  
#  # a nucleotide example
#  seq_example <- "ACCTGGAATTC"
#  
#  randomSeqs(seq = seq_example, sample_size = 10)
#  

## ----eval=FALSE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
#  # a protein example
#  seq_example <- "NPPAAM"
#  
#  randomSeqs(seq = seq_example, sample_size = 10)
#  

## ----eval=FALSE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
#  seq_example <- "MEDQVGFGF"
#  subject_example <- "AYAIDPTPAF"
#  
#  p_val_align <- evalAlignment(seq_example, subject_example,sample_size = 10,
#                               Biostrings::pairwiseAlignment, scoreOnly = TRUE,
#                               fit_distr = "norm", comp_cores = 1)
#  
#  p_val_align
#  

## ----eval=FALSE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
#  
#  Biostrings::pairwiseAlignment(seq_example, subject_example)
#