| maskMotif {Biostrings} | R Documentation |
Functions for masking a sequence by content (or by position).
maskMotif(x, motif, min.block.width=1, ...) mask(x, start=NA, end=NA, pattern)
x |
The sequence to mask. |
motif |
The motif to mask in the sequence. |
min.block.width |
The minimum width of the blocks to mask. |
... |
Additional arguments for |
start |
An integer vector containing the starting positions of the regions to mask. |
end |
An integer vector containing the ending positions of the regions to mask. |
pattern |
The motif to mask in the sequence. |
A MaskedXString object for maskMotif
and an XStringViews object for mask.
H. Pagès
read.Mask,
matchPattern,
XString-class,
MaskedXString-class,
XStringViews-class,
MaskCollection-class
## ---------------------------------------------------------------------
## EXAMPLE 1
## ---------------------------------------------------------------------
maskMotif(BString("AbcbbcbEEE"), "bcb")
maskMotif(BString("AbcbcbEEE"), "bcb")
## maskMotif() can be used in an incremental way to mask more than 1
## motif. Note that maskMotif() does not try to mask again what's
## already masked (i.e. the new mask will never overlaps with the
## previous masks) so the order in which the motifs are masked actually
## matters as it will affect the total set of masked positions.
x0 <- BString("AbcbEEEEEbcbbEEEcbbcbc")
x1 <- maskMotif(x0, "E")
x1
x2 <- maskMotif(x1, "bcb")
x2
x3 <- maskMotif(x2, "b")
x3
## Note that inverting the order in which "b" and "bcb" are masked would
## lead to a different final set of masked positions.
## Also note that the order doesn't matter if the motifs to mask don't
## overlap (we assume that the motifs are unique) i.e. if the prefix of
## each motif is not the suffix of any other motif. This is of course
## the case when all the motifs have only 1 letter.
## ---------------------------------------------------------------------
## EXAMPLE 2
## ---------------------------------------------------------------------
x <- DNAString("ACACAACTAGATAGNACTNNGAGAGACGC")
## Mask the N-blocks
x1 <- maskMotif(x, "N")
x1
as(x1, "Views")
gaps(x1)
as(gaps(x1), "Views")
## Mask the AC-blocks
x2 <- maskMotif(x1, "AC")
x2
gaps(x2)
## Mask the GA-blocks
x3 <- maskMotif(x2, "GA", min.block.width=5)
x3 # masks 2 and 3 overlap
gaps(x3)
## ---------------------------------------------------------------------
## EXAMPLE 3
## ---------------------------------------------------------------------
library(BSgenome.Dmelanogaster.UCSC.dm3)
chrU <- Dmelanogaster$chrU
chrU
alphabetFrequency(chrU)
chrU <- maskMotif(chrU, "N")
chrU
alphabetFrequency(chrU)
as(chrU, "Views")
as(gaps(chrU), "Views")
mask2 <- Mask(mask.width=length(chrU),
start=c(50000, 350000, 543900), width=25000)
names(mask2) <- "some ugly regions"
masks(chrU) <- append(masks(chrU), mask2)
chrU
as(chrU, "Views")
as(gaps(chrU), "Views")
## ---------------------------------------------------------------------
## EXAMPLE 4
## ---------------------------------------------------------------------
## Note that unlike maskMotif(), mask() returns an XStringViews object!
## masking "by position"
mask("AxyxyxBC", 2, 6)
## masking "by content"
mask("AxyxyxBC", "xyx")
noN_chrU <- mask(chrU, "N")
noN_chrU
alphabetFrequency(noN_chrU, collapse=TRUE)