libscheme: Get the specified library scheme

In peptider: Evaluation of Diversity in Nucleotide Libraries

Description

Get the specified library scheme

Usage

libscheme(schm, k = 1)

Arguments

schm	either a character vector giving the name of a built-in scheme, or a data frame consisting of the scheme definition
k	length of peptide sequences

Value

list consisting of a data frame of peptide classes, size of class, and its probabilities, and a list of additional information relating to the library scheme

Examples

libscheme("NNN")
libscheme("NNK", 2)

# Build a custom 20/20 library
custom <- data.frame(class = c("A", "Z"), aacid = c("SLRAGPTVIDEFHKNQYMW", "*"), c = c(1, 0))
libscheme(custom)

Example output

$data
      class di choices      probs
1 1,0,0,0,0  3       1 0.29508197
2 0,1,0,0,0  5       1 0.32786885
3 0,0,1,0,0  1       1 0.04918033
4 0,0,0,1,0  9       1 0.29508197
5 0,0,0,0,1  2       1 0.03278689

$info
$info$nucleotides
[1] 64

$info$valid
[1] 61

$info$scheme
  class     aacid c s
1     A       SLR 6 3
2     B     AGPTV 4 5
3     C         I 3 1
4     D DEFHKNQYC 2 9
5     E        MW 1 2
6     Z         * 3 1


$data
  class  di choices      probs
1 2,0,0   9       1 0.08428720
2 1,1,0  15       2 0.09365245
3 0,2,0  25       1 0.10405827
4 1,0,1  36       2 0.11238293
5 0,1,1  60       2 0.12486993
6 0,0,2 144       1 0.14984391

$info
$info$nucleotides
[1] 32

$info$valid
[1] 31

$info$scheme
  class        aacid c  s
1     A          SLR 3  3
2     B        AGPTV 2  5
3     C DEFHIKMNQWYC 1 12
4     Z            * 1  1


$data
  class di choices probs
1     1 19       1     1

$info
$info$nucleotides
[1] 19

$info$valid
[1] 19

$info$scheme
  class               aacid c  s
1     A SLRAGPTVIDEFHKNQYMW 1 19
2     Z                   * 0  1

peptider documentation built on May 2, 2019, 2:43 a.m.