n2s: function to convert the numeric encoding of a DNA sequence...

In seqinr: Biological Sequences Retrieval and Analysis

function to convert the numeric encoding of a DNA sequence into a vector of characters

Description

By default, if no ‘levels’ arguments is provided, this function will just transform your vector of integer into a DNA sequence according to the lexical order: 0 -> "a", 1 -> "c", 2 -> "g", 3 -> "t", others -> NA.

Usage

n2s(nseq, levels = c("a", "c", "g", "t"), base4 = TRUE)

Arguments

nseq	A vector of integers
levels	the translation vector
base4	when this logical is true, the numerical encoding of levels starts at 0, when it is false the numerical encoding of levels starts at 1.

Value

a vector of characters

Author(s)

J.R. Lobry

References

citation("seqinr")

See Also

s2n

Examples

##example of the default behaviour:
nseq <- sample(x = 0:3, size = 100, replace = TRUE)
n2s(nseq) 
# Show what happens with out-of-range and NA values:
nseq[1] <- NA
nseq[2] <- 777
n2s(nseq)[1:10]
# How to get an RNA instead:
n2s(nseq, levels = c("a", "c", "g", "u"))

seqinr documentation built on May 29, 2024, 6:36 a.m.