| mask {Biostrings} | R Documentation |
Use this function to mask some portions of a sequence. The portions to mask can either be specified "by position" (start/end) or "by content" (they match a given pattern).
mask(x, ...)
x |
The single string or BString (or derived) object to mask. This can also be a BStringViews object. |
... |
Additional arguments to be passed to or from methods. |
For BString (or derived) objects, mask() can be used in two
different ways: by specifying the starts/ends of the portions to mask
(masking "by position") or by specifying a pattern (masking "by content").
For BStringViews objects, no extra argument is needed: y <- mask(x)
is the shortest (in term of number of views) BStringViews object such that:
(a) subject(y) == subject(x),
(b) y views cover the portions of the subject that are not covered by x
views,
(c) y views are sorted from left to right,
(d) y views are not "out of limits".
A BStringViews object containing the set of "unmasked" portions.
H. Pages
BStringViews, BString, DNAString, RNAString
## masking "by position"
mask("AxyxyxBC", 2, 6)
## masking "by content"
mask("AxyxyxBC", "xyx")
## masking the N's in a chromosome sequence
library(BSgenome.Dmelanogaster.FlyBase.r51)
chrU <- Dmelanogaster[["U"]]
alphabetFrequency(chrU)
noN_chrU <- mask(chrU, "N")
alphabetFrequency(noN_chrU)
## masking a BStringViews object
mask(noN_chrU)
v <- views("AxyxyxBC", c(6, 4,-1, NA), c(7, 6, 1, 1))
mask(v)
## note that applying mask() again returns a BStringViews object
## where the original views on v have been merged, sorted from left to right
## and cleaned from their "out of limits" portions
mask(mask(v))
## finally, note that mask(mask(mask(v))) is _always_ the same as mask(v)
mask(mask(mask(v)))