ContactMatrix sorting {InteractionSet} | R Documentation

## ContactMatrix sorting and ordering

### Description

Methods to sort and order ContactMatrix objects, based on the anchor indices. Also, methods to remove duplicate rows or columns in each ContactMatrix.

### Usage

    ## 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, ...)

### Arguments

`...` | For `sort,ContactMatrix-method`, one or more ContactMatrix objects with the same dimensions. Otherwise, ignored in all other methods.
`x` | A ContactMatrix object.
`na.last` | A logical scalar indicating whether `NA` values should be ordered last. This should not be relevant as anchor indices should be finite.
`decreasing` | A logical scalar indicating whether sorting should be performed in decreasing order.
`incomparables` | A logical scalar, ignored.
`fromLast` | A logical scalar indicating whether the last entry of a repeated set in `x` should be considered as a non-duplicate.

### Details

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 `anchor2` slot. 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 `decreasing=TRUE`.

`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 `x`. 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 `anchor1` slot. The second does the same for columns based on the `anchor2` slot. 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 `x`. This is equivalent to subsetting based on the non-duplicate rows and columns defined in `duplicated,ContactMatrix-method`.

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.

### Value

For `sort` and `unique`, a ContactMatrix object is returned with sorted or unique rows/columns, respectively.

For `order`, a list of two integer vectors is returned containing row/column permutations.

For `duplicated`, a list of logical vectors is returned specifying which rows/columns are duplicated.

### Author(s)

Aaron Lun

### See Also

`ContactMatrix-class`

### Examples

    example(ContactMatrix, echo=FALSE)

    anchors(x)
    x2 <- sort(x)
    x2
    anchors(x2)

    # Can also order them.
    o <- order(x)
    o
    stopifnot(all.equal(x[o$row,o$column], x2))

    # Checking duplication.
    duplicated(x)
    duplicated(rbind(x, x))
    stopifnot(all.equal(unique(x), unique(rbind(x, x))))

[Package InteractionSet version 1.12.0 Index]