ContactGroup-class: Class '"ContactGroup"'

In hansenlab/bnbc: Bandwise normalization and batch correction of Hi-C data

Class "ContactGroup"

Description

The ContactGroup class represents a collection of contact matrices which are observations from different samples on the same set of genomic loci.

Usage

ContactGroup(rowData, contacts, colData)

Arguments

rowData	Object of class GenomicRanges equal in length to the number of rows/columns in contact matrices.
contacts	Object of class list that contains all contact matrices.
colData	Object of class DataFrame containing sample-level information.

Details

The ContactGroup class contains a set of contact matrices in the slot 'contacts'. All matrices are required to be of the same dimensionality. 'ContactGroup()' expects a list of symmetric matrices to be passed to the contstructor. Data about these contact matrices is held in two other slots. Data about the genomic loci represented in the ContactGroup is found in the 'rowData' slot as a GenomicRanges objects, and sample-level information is located in the 'colData' slot as a DataFrame.

Value

A ContactGroup object.

Methods

In the code snippets below, x is a ContactGroup object.

[

signature(x = "ContactGroup", i = "ANY", j = "ANY", drop = "ANY"): Allows for subsetting the contact matrices through use of i or of samples through j.

colData

signature(x = "ContactGroup"): Get sample-level information about samples in x

colData<-

signature(x = "ContactGroup", value = "DataFrame"): Set sample-level information about samples in x. value is expected to be a DataFrame object.

dim

signature(x = "ContactGroup"): Obtain the dimensions of a ContactGroup. Returns 2 values: one representing the number of bins in the contact matrices and another representing the number of samples.

rowData

signature(x = "ContactGroup"): Get the GenomicRanges object describing the loci in the ContactGroup. value is expected to be a GenomicRanges object.

rowData<-

signature(x = "ContactGroup"): Set the GenomicRanges object describing the bins in the ContactGroup. value is expected to be a GenomicRanges object.

show

signature(object = "ContactGroup"): Method to display summary information about a ContactGroup: the number of bins, the width of the bins and the number of samples.

librarySize

signature(x = "ContactGroup"): Method to compute the library size of each contact matrix in x. Library size is defined to be the sum of the upper triangle of a contact matrix.

logCPM

signature(x = "ContactGroup"): Method to transform each contact matrix to logCPM scale.

Utilities

contacts

contacts(x), contacts(x) <- value: Method to extract the list of contact matrices from a ContactGroup. value is expected to be a list object.

distanceIdx

signature(cg = "ContactGroup", threshold="ANY", step="ANY"): Method to identify which matrix bands are no more than threshold bins apart, where each bin represents step base pairs.

References

Law, C.W., Chen, Y., Shi, W. and Smyth G.K. voom: Precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biology 2014, 15:R29. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1186/gb-2014-15-2-r29")}.

Examples

data(cgEx)

cgEx[1,]
cgEx[,1]

cd <- colData(cgEx)
colData(cgEx) <- cd

gr <- rowData(cgEx)
rowData(cgEx) <- gr

cgEx

cl <- contacts(cgEx)
contacts(cgEx) <- cl

d.idx <- distanceIdx(cgEx, 1e7, 4e4)

libs <- librarySize(cgEx)

cgEx.cpm <- logCPM(cgEx)

## below, upper.mats.list is a list of upper triangular matrices
## SampleData is a DataFrame of sample data and LociData is a GenomicRanges objec
## Not run: 
  MatsList <- lapply(upper.mats.list, function(M) M[lower.tri(M)] = M[upper.tri(M)])
  cg <- ContactGroup(LociData, MatsList, SampleData)

## End(Not run)

hansenlab/bnbc documentation built on Feb. 4, 2024, 7:20 a.m.