ModStringSet objects

The ModStringSet class is a container for storing a set of ModString objects. It follows the same principles as the other XStringSet objects.

As usual the ModStringSet containers derive directly from the XStringSet virtual class.

The ModStringSet class is in itself a virtual class with two types of derivates:

• ModDNAStringSet

• ModRNAStringSet

Each class can only be converted to its parent DNAStringSet or RNAStringSet. The modified nucleotides will be converted to their original nucleotides.

Please note, that due to encoding issues not all modifications can be instanciated directly from the console. The vignette contains a comphrensive explanation and examples for working around the problem.

ModDNAStringSet(
  x = character(),
  start = NA,
  end = NA,
  width = NA,
  use.names = TRUE
)

ModRNAStringSet(
  x = character(),
  start = NA,
  end = NA,
  width = NA,
  use.names = TRUE
)

Arguments

x

Either a character vector (with no NAs), or an ModString, ModStringSet or ModStringViews object.

start, end, width

Either NA, a single integer, or an integer vector of the same length as x specifying how x should be "narrowed" (see ?narrow for the details).

use.names

TRUE or FALSE. Should names be preserved?

Value

a ModStringSet object.

Examples

# Constructing ModDNAStringSet containing an m6A
m1 <- ModDNAStringSet(c("AGCT`","AGCT`"))
m1
#>   A ModDNAStringSet instance of length 2
#>     width seq
#> [1]     5 AGCT`
#> [2]     5 AGCT`

# converting to DNAStringSet

# Constructing ModRNAStringSet containing an m6A
m2 <- ModRNAStringSet(c("AGCU`","AGCU`"))
m2
#>   A ModRNAStringSet instance of length 2
#>     width seq
#> [1]     5 AGCU`
#> [2]     5 AGCU`