seqinr (version 1.0-1)

n2s: 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

References

� To have an overview of the seqinR's functionnality, please consult this vignette: Charif, D., Lobry, J.R. (2005) SeqinR: a contributed package to the R project for statistical computing devoted to biological sequences retrieval and analysis. Springer Verlag, Biological and Medical Physics/Biomedical Series, in preparation.

See Also

s2n

Examples

##example of the default behaviour:
nseq <- sample(x = 0:3, size = 100, replace = TRUE)
n2s(nseq) 
# Show what's happen 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"))