| comp {seqinr} | R Documentation |
Complements a sequence, for instance if the sequence is
"a","c","g","t" it returns "t","g","c","a".
This is not the reverse complementary strand. This function
can handle ambiguous bases if required.
comp(seq, forceToLower = TRUE, ambiguous = FALSE)
seq |
a DNA sequence as a vector of single chars |
forceToLower |
if TRUE character in seq are forced to lower case |
ambiguous |
if TRUE ambiguous bases in seq are handled |
a vector of characters which is the complement of the sequence, not the reverse complementary strand. Undefined values are returned as NA.
D. Charif, J.R. Lobry
citation("seqinr")
Because ssDNA sequences are always written in the 5'->3'
direction, use rev(comp(seq)) to get the reverse complementary
strand (see rev).
##
## Show that comp() does not return the reverve complementary strand:
##
c2s(comp(s2c("aaaattttggggcccc")))
##
## Show how to get the reverse complementary strand:
##
c2s(rev(comp(s2c("aaaattttggggcccc"))))
##
## Show what happens with non allowed values:
##
c2s(rev(comp(s2c("aaaaXttttYggggZcccc"))))
##
## Show what happens with ambiguous bases:
##
allbases <- s2c("abcdghkmstvwn")
comp(allbases) # NA are produced
comp(allbases, ambiguous = TRUE) # No more NA
##
## Routine sanity check:
##
stopifnot(identical(comp(allbases, ambiguous = TRUE), s2c("tvghcdmksabwn")))