MaskCollection-class {IRanges} | R Documentation |
MaskCollection objects
Description
The MaskCollection class is a container for storing a collection of masks that can be used to mask regions in a sequence.
Details
In the context of the Biostrings package, a mask is a set of regions
in a sequence that need to be excluded from some computation.
For example, when calling alphabetFrequency
or matchPattern
on a chromosome sequence,
you might want to exclude some regions like the centromere or the repeat
regions. This can be achieved by putting one or several masks on the sequence
before calling alphabetFrequency
on it.
A MaskCollection object is a vector-like object that represents such set of masks. Like standard R vectors, it has a "length" which is the number of masks contained in it. But unlike standard R vectors, it also has a "width" which determines the length of the sequences it can be "put on". For example, a MaskCollection object of width 20000 can only be put on an XString object of 20000 letters.
Each mask in a MaskCollection object x
is just a finite set of
integers that are >= 1 and <= width(x)
.
When "put on" a sequence, these integers indicate the positions of the
letters to mask.
Internally, each mask is represented by a NormalIRanges
object.
Basic accessor methods
In the code snippets below, x
is a MaskCollection object.
length(x)
:-
The number of masks in
x
. width(x)
:-
The common with of all the masks in
x
. This determines the length of the sequences thatx
can be "put on". active(x)
:-
A logical vector of the same length as
x
where each element indicates whether the corresponding mask is active or not. names(x)
:-
NULL
or a character vector of the same length asx
. desc(x)
:-
NULL
or a character vector of the same length asx
. nir_list(x)
:-
A list of the same length as
x
, where each element is a NormalIRanges object representing a mask inx
.
Constructor
Mask(mask.width, start=NULL, end=NULL, width=NULL)
:-
Return a single mask (i.e. a MaskCollection object of length 1) of width
mask.width
(a single integer >= 1) and masking the ranges of positions specified bystart
,end
andwidth
. See theIRanges
constructor (?IRanges
) for howstart
,end
andwidth
can be specified. Note that the returned mask is active and unnamed.
Other methods
In the code snippets below, x
is a MaskCollection object.
isEmpty(x)
:-
Return a logical vector of the same length as
x
, indicating, for each mask inx
, whether it's empty or not. max(x)
:-
The greatest (or last, or rightmost) masked position for each mask. This is a numeric vector of the same length as
x
. min(x)
:-
The smallest (or first, or leftmost) masked position for each mask. This is a numeric vector of the same length as
x
. maskedwidth(x)
:-
The number of masked position for each mask. This is an integer vector of the same length as
x
where all values are >= 0 and <=width(x)
. maskedratio(x)
:-
maskedwidth(x) / width(x)
Subsetting and appending
In the code snippets below,
x
and values
are MaskCollection objects.
x[i]
:-
Return a new MaskCollection object made of the selected masks. Subscript
i
can be a numeric, logical or character vector. x[[i, exact=TRUE]]
:-
Extract the mask selected by
i
as a NormalIRanges object. Subscripti
can be a single integer or a character string. append(x, values, after=length(x))
:-
Add masks in
values
tox
.
Other methods
In the code snippets below, x
is a MaskCollection object.
collapse(x)
:-
Return a MaskCollection object of length 1 obtained by collapsing all the active masks in
x
.
Author(s)
Hervé Pagès
See Also
NormalIRanges-class,
read.Mask,
MaskedXString-class,
reverse
,
alphabetFrequency
,
matchPattern
Examples
## Making a MaskCollection object:
mask1 <- Mask(mask.width=29, start=c(11, 25, 28), width=c(5, 2, 2))
mask2 <- Mask(mask.width=29, start=c(3, 10, 27), width=c(5, 8, 1))
mask3 <- Mask(mask.width=29, start=c(7, 12), width=c(2, 4))
mymasks <- append(append(mask1, mask2), mask3)
mymasks
length(mymasks)
width(mymasks)
collapse(mymasks)
## Names and descriptions:
names(mymasks) <- c("A", "B", "C") # names should be short and unique...
mymasks
mymasks[c("C", "A")] # ...to make subsetting by names easier
desc(mymasks) <- c("you can be", "more verbose", "here")
mymasks[-2]
## Activate/deactivate masks:
active(mymasks)["B"] <- FALSE
mymasks
collapse(mymasks)
active(mymasks) <- FALSE # deactivate all masks
mymasks
active(mymasks)[-1] <- TRUE # reactivate all masks except mask 1
active(mymasks) <- !active(mymasks) # toggle all masks
## Other advanced operations:
mymasks[[2]]
length(mymasks[[2]])
mymasks[[2]][-3]
append(mymasks[-2], gaps(mymasks[2]))