Using the DIList class to store pairwise genomic interactions.
NOTE: this class has been deprecated in favour of the InteractionSet class from the InteractionSet package.
Users should use InteractionSet objects for future work.
Existing DIList objects can be converted into InteractionSet objects using the DI2IS function.
Details
Each DIList stores counts for pairwise genomic interactions.
Slots are defined as:
counts:
an integer matrix containing the number of read pairs for an interaction in each library
colData:
a DataFrame object containing library-specific information in each row, e.g., the total number of read pairs
exptData:
a List object containing data or parameters pertinent to counting
anchors:
an integer vector specifying the index of the first interacting region
targets:
an integer vector specifying the index of the second interacting region
regions:
a GRanges object containing the coordinates of all interacting regions
Each row of counts corresponds to an interaction, while each column corresponds to a library.
Each interaction is parameterized by an anchors and targets index, pointing to the anchor and target intervals in regions, respectively.
The anchor interval is defined as that with the higher genomic start coordinate, compared to that of the target interval.
This means that anchors is never less than targets to avoid redundant permutations.
Constructor
DIList(counts, totals=colSums(counts), anchors, targets, regions, exptData=List(), ...):
Returns a DIList object where each entry is used to fill the corresponding slots.
Type coercion is performed as required.
Arguments in ... are used as columns in colData.
Accessors
In the code snippets below, x is a DIList object.
anchors(x, id=FALSE):
Get the GRanges corresponding to the anchor intervals for each interaction.
If id=TRUE, indices to the corresponding intervals in regions are returned instead.
targets(x, id=FALSE):
Get the GRanges corresponding to the target intervals for each interaction.
If id=TRUE, indices to the corresponding intervals in regions are returned instead.
regions(x):
Get the GRanges for all interacting regions.
counts(x):
Get the matrix of counts for all interactions in all libraries.
colData(x):
Get the DataFrame of library-specific information.
exptData(x):
Get the List of experiment-specific information.
x$name:
Get the value of colData(x)$name.
dim(x):
Get the dimensions, i.e., number of interactions (rows) against number of libraries (columns).
dimnames(x):
Get the dimension names. This returns a list of length 2, where each element is NULL or a character vector.
Modifiers
In the code snippets below, x is a DIList object.
x$name <- value:
Assign value to the name field of the colData in x.
Primarily intended for modification of the library sizes in totals, but can also be used to store additional library-specific information.
exptData(x) <- value:
Assign a SimpleList object named value to the exptData slot of x.
Note that this also works with list accessors, e.g., by assigning to exptData(x)$name.
Subsetting and combining
In the code snippets below, x is a DIList object.
x[i, j]:
Get count and coordinate data for all interactions i in libraries j.
Either i or j can be missing, in which case all interactions or libraries are returned, respectively.
c(x, ..., add.totals=TRUE):
Merge x with other DIList objects in ..., by concatenating the count matrices along with the anchor and target indices.
By default, the totals will be added across all objects to be merged.
This can be turned off by setting add.totals=FALSE, whereby only the totals of x are used (a warning will be generated if totals are not identical between objects).
In all cases, objects to be merged should have the same value in the regions slot.
Other methods
In the code snippets below, x is a DIList object.
show(x):
Shows a summary of the information in x.
Specifically, a string is printed that reports the number of libraries, number of interactions and total number of regions in x.
as.matrix(x, first=NULL, second=first, fill=NULL, ...):
Converts x into a contact matrix where rows and columns represent regions on the first and second chromosomes, respectively.
Entries of the matrix correspond to an interaction of x.
Each entry is extracted from fill, where fill is a numeric vector with one value per interaction in x.
By default, the average abundance of each interaction in x is used as the entry.
For intra-chromosomal spaces, both sides of the diagonal are filled.
Multiple chromosomes can also be specified in first or second (all chromosomes are used by default).
Each row and column is named according to the matching index of regions(x).
providing 
.