Methods to sort and order ContactMatrix objects, based on the anchor indices. Also, methods to remove duplicate rows or columns in each ContactMatrix.
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## S4 method for signature 'ContactMatrix' order(..., na.last=TRUE, decreasing=FALSE) ## S4 method for signature 'ContactMatrix' sort(x, decreasing=FALSE, ...) ## S4 method for signature 'ContactMatrix' duplicated(x, incomparables=FALSE, fromLast=FALSE, ...) ## S4 method for signature 'ContactMatrix' unique(x, incomparables=FALSE, fromLast=FALSE, ...)
A ContactMatrix object.
A logical scalar indicating whether
A logical scalar indicating whether sorting should be performed in decreasing order.
A logical scalar, ignored.
A logical scalar indicating whether the last entry of a repeated set in
Sorting is performed based on the anchor indices of the ContactMatrix object.
Rows are ordered for increasing values of the
anchor1 slot, while columns are ordered for increasing values of the
This equates to ordering by the coordinates directly, as the GRanges in the
regions slot is always sorted.
Based on this,
sort,ContactMatrix-method will return a sorted copy of
x with permuted rows/columns in increasing order.
This can be set to decreasing order by specifying
order,ContactMatrix-method returns a list of 2 integer vectors.
The first vector contains the permutation to rearrange the rows of
x in increasing order, while the second vector does the same for the columns of
If multiple objects are supplied to
order, ordering will be computed using anchor indices from successive objects.
In other words, ordering will be performed using anchor indices from the first object;
any rows with the same
anchor1 or columns with the same
anchor2 will be split using the corresponding indices in the second object; and so on.
duplicated,ContactMatrix-method returns a list of two logical vectors.
The first vector indicates whether rows are duplicated, based on identical values in the
The second does the same for columns based on the
For a set of duplicated rows or columns, the first occurrence of that row/column is marked as the non-duplicate if
fromLast=FALSE, and the last entry otherwise.
unique,ContactMatrix-method returns an ContactMatrix object where all duplicate rows and columns have been removed from
This is equivalent to subsetting based on the non-duplicate rows and columns defined in
Note that sorting and duplicate identification only use the anchor indices.
The values of the
matrix slot are not used in distinguishing between rows or columns with the same index.
unique, a ContactMatrix object is returned with sorted or unique rows/columns, respectively.
order, a list of two integer vectors is returned containing row/column permutations.
duplicated, a list of logical vectors is returned specifying which rows/columns are duplicated.
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