"inflate"(x, rows, columns, fill, swap=TRUE, sparse=FALSE, ...)
"inflate"(x, rows, columns, assay=1L, sample=1L, fill=NULL, swap=TRUE, sparse=FALSE, ...)
"deflate"(x, collapse=TRUE, extract, use.zero, use.na, ...)inflate, or a ContactMatrix object for deflate.
If it is an integer vector, it is assumed to refer to intervals in the regions slot of x.
Values of the vector need not be sorted or collapse, but must lie within [1, regions(x)].
If it is a character vector, it is assumed to contain the names of the reference sequences of interest (i.e., chromosome names).
If it is a GRanges object, overlapsAny will be called to identify the overlapping intervals of the regions slot.
nrow(x), containing values with which to fill the ContactMatrix.
If specified, this overrides extraction of assay values for inflate,InteractionSet-method.
x prior to deflation.
x to convert into pairwise interactions.
NA entries into pairwise interactions.
inflate, additional arguments to pass to overlapsAny when rows or columns is a GRanges. For deflate, additional arguments to pass to the InteractionSet constructor.
inflate, a ContactMatrix is returned.For deflate, an InteractionSet object is returned.
inflate method will return a ContactMatrix where the rows and columns correspond to specified regions of interest in rows and columns.
For the GInteractions method, values in the matrix are filled based on user-supplied values in fill.
Each entry of fill corresponds to an interaction in x is used to set the matrix value at the matching row/column.
Some entries of the matrix will correspond to pairwise interactions that are not present in x - these are filled with NA values. By default, filling is repeated after swapping the anchor indices.
This means that the value of the matrix at (1, 2) will be the same as that at (2, 1), i.e., the matrix is symmetric around the diagonal of the interaction space.
However, if swap=FALSE, filling is performed so that the first and second anchor indices correspond strictly to rows and columns, respectively.
This may be preferable if the order of the anchors contains some relevant information.
In all cases, if duplicated interactions are present in x (and redundant permutations, when swap=TRUE), one will be arbitrarily chosen to fill the matrix. For the InteractionSet inflate method, entries in the matrix are filled in based on the values in the first sample of the first assay by default.
For more complex x, values from different assays and samples can be extracted using the assay and sample arguments.
Note that if fill is specified, it will override any extraction of values from the assays. If sparse=TRUE, inflate will return a ContactMatrix containing a sparseMatrix in the matrix slot.
Here, entries without a corresponding interaction in x are set to zero, not NA.deflate method will return an InteractionSet where each relevant entry in the ContactMatrix is converted into a pairwise interaction.
Relevant entries are defined as those that are non-zero, if use.zero is FALSE; and non-NA, if use.na is FALSE.
If x contains a sparseMatrix representation, the former is set to FALSE while the latter is set to TRUE, if either are not specified.
For all other matrices, use.zero=TRUE and use.na=FALSE by default. If extract is specified, this overrides all values of use.zero and use.na.
A typical application would be to deflate a number of ContactMatrix objects with the same extract matrix.
This ensures that the resulting InteractionSet objects can be easily combined with cbind, as the interactions are guaranteed to be the same.
Otherwise, different interactions may be extracted depending on the presence of zero or NA values. The values of all matrix entries are stored as a one-sample assay, with each value corresponding to its pairwise interaction after conversion.
Duplicate interactions are removed by default, along with redundant permutations of the anchor indices.
These can be included in the returned object by setting collapse=FALSE.
Additional arguments can be used to specify the colData and metadata, which are stored in the ContactMatrix itself.fill.
The majority of these values are likely to be zero just because there was no corresponding interaction in x to set it to a non-zero value. Whether or not this is a problem depends on the application.
For example, if fill represents count data and only interactions with non-zero counts are stored in x, then setting all other entries to zero is sensible.
However, in other cases, it is not appropriate to fill entries corresponding to missing interactions with zero.
If fill represents, e.g., log-fold changes, then setting missing entries to a value of zero will be misleading.
One could simply ignore zeroes altogether, though this will also discard entries that are genuinely zero. These problems are largely avoided with the default denseMatrix classes, where missing entries are simply set to NA.InteractionSet-class,
GInteractions-class,
ContactMatrix-class,
sparseMatrix-class
example(InteractionSet, echo=FALSE)
inflate(iset, 1:10, 1:10)
inflate(iset, 1:10, 1:10, sparse=TRUE)
inflate(iset, 1:10, 1:5+10)
inflate(iset, "chrA", 1:5+10)
inflate(iset, "chrA", "chrB")
inflate(iset, "chrA", GRanges("chrB", IRanges(1, 10)))
y <- inflate(iset, 1:10, 1:10)
iset2 <- deflate(y)
iset2
assay(iset2)
y <- inflate(iset, 1:10, 1:10, swap=FALSE)
iset2 <- deflate(y)
iset2
assay(iset2)
# Testing with different fillings:
y <- inflate(iset, 1:10, 1:10, sample=2)
iset2 <- deflate(y)
assay(iset2)
y <- inflate(iset, 1:10, 1:10, fill=rowSums(assay(iset)))
iset2 <- deflate(y)
assay(iset2)
y2 <- inflate(interactions(iset), 1:10, 1:10, rowSums(assay(iset)))
identical(y, y2) # should be TRUE
# Effect of 'collapse'
y <- inflate(iset, c(8, 1:10), 1:10)
deflate(y)
deflate(y, collapse=FALSE)
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