Description Usage Arguments Details Value Author(s) See Also Examples

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

1 2 3 4 5 6 7 8 | ```
## 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, ...)
``` |

`...` |
For |

`x` |
A ContactMatrix object. |

`na.last` |
A logical scalar indicating whether |

`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 |

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.

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.

Aaron Lun

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 |

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