replaceLetterAt {Biostrings} | R Documentation |
replaceLetterAt
first makes a copy of a sequence and then
replaces the original letters by new letters at some specified locations
in the copied sequence.
.inplaceReplaceLetterAt
is the IN PLACE version of
replaceLetterAt
: it will modify the original
sequence in place i.e. without copying it first.
Note that in place modification of a sequence is fundamentally
dangerous because it alters all objects defined in your session
that make reference to the modified sequence.
NEVER use .inplaceReplaceLetterAt
, unless you know what
you are doing!
replaceLetterAt(x, at, letter, if.not.extending="replace", verbose=FALSE) ## NEVER USE THIS FUNCTION! .inplaceReplaceLetterAt(x, at, letter)
x |
A DNAString object. |
at |
An integer vector with no NAs specifying the locations where the replacements must occur. Note that locations can be repeated and in this case the last replacement to occur at a given location prevails. |
letter |
Character vector with no NAs. The total number of letters in letter
(sum(nchar(letter)) ) must be equal to the number of locations
(length(at) ).
|
if.not.extending |
What to do if the new letter is not "extending" the old letter?
The new letter "extends" the old letter if both are IUPAC letters
and the new letter is as specific or less specific than the old
one (e.g. M extends A, Y extends Y, but Y doesn't extend S).
Possible values are "replace" (the default) for replacing
in all cases, "skip" for not replacing when the new letter
does not extend the old letter, "merge" for merging the new
IUPAC letter with the old one, and "error" for raising
an error.
Note that the gap ( "-" ) and hard masking ("+" )
letters are not extending or extended by any other letter.
Also note that "merge" is the only value for the
if.not.extending argument that guarantees the final result
to be independent on the order the replacement is performed (although
this is only relevant when at contains duplicated locations,
otherwise the result is of course always independent on the order,
whatever the value of if.not.extending is).
|
verbose |
When TRUE , a warning will report the number of skipped or merged
letters.
|
.inplaceReplaceLetterAt
semantic is equivalent to calling
replaceLetterAt
with if.not.extending="merge"
and verbose=FALSE
.
Never use .inplaceReplaceLetterAt
!
It is used by the injectSNPs
function
in the BSgenome package, as part of the "lazy sequence loading"
mechanism, for altering the original sequences of a
BSgenome object at "sequence-load time".
This alteration consists in injecting the IUPAC ambiguity letters
representing the SNPs into the just loaded sequence, which is the
only time where in place modification of the external data of
an XString object is safe.
A DNAString object of the same length as the orignal object x
for replaceLetterAt
.
H. Pages
IUPAC_CODE_MAP
,
chartr
,
injectHardMask
,
DNAString,
injectSNPs
,
BSgenome
replaceLetterAt(DNAString("AAMAA"), c(5, 1, 3, 1), "TYNC") replaceLetterAt(DNAString("AAMAA"), c(5, 1, 3, 1), "TYNC", if.not.extending="merge")