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The Fragment class

Source: R/classes.R, R/fragments.R
Fragment2-class.Rd

The Fragment class is designed to hold information needed for working with fragment files.

Usage

# S4 method for class 'Fragment2'
seqlevels(x)

# S4 method for class 'Fragment2'
seqlevels(x) <- value

# S4 method for class 'Fragment2'
seqlevelsStyle(x)

# S4 method for class 'Fragment2'
seqlevelsStyle(x) <- value

# S4 method for class 'Fragment2'
renameSeqlevels(x, value)

Arguments

x

A Fragment2 object

value

A named character vector or name of a seqlevelsStyle

Functions

  • seqlevels(Fragment2): Get sequence levels

  • seqlevels(Fragment2) <- value: Set sequence levels

  • seqlevelsStyle(Fragment2): Get sequence levels style

  • seqlevelsStyle(Fragment2) <- value: Set sequence levels style

  • renameSeqlevels(Fragment2): Rename sequence levels

Slots

file.path

Path to the fragment file on disk.

file.index

Path to the fragment file index on disk.

hash

A vector of two md5sums: first element is the md5sum of the fragment file, the second element is the md5sum of the index.

cells

A named vector of cells where each element is the cell barcode as it appears in the fragment file, and the name of each element is the corresponding cell barcode as stored in the ChromatinAssay5 object.

seqlevels

A named vector of sequence levels (eg, chromosome name) where each element is the sequence name as it appears in the fragment file, and then name of each element is the corresponding sequence name as stored in the ChromatinAssay5 object.