LinkedPairs-class: Tables of where syntenic hits link pairs of genes
In npcooley/SynExtend: Tools for Working With Synteny Objects

LinkedPairs

R Documentation

Tables of where syntenic hits link pairs of genes

Description

Syntenic blocks describe where order is shared between two sequences. These blocks are made up of exact match hits. These hits can be overlayed on the locations of sequence features to clearly illustrate where exact sequence similarity is shared between pairs of sequence features.

Usage

## S3 method for class 'LinkedPairs'
print(x,
      quote = FALSE,
      right = TRUE,
      ...)

Arguments

`x`	An object of class `LinkedPairs`.
`quote`	Logical indicating whether to print the output surrounded by quotes.
`right`	Logical specifying whether to right align strings.
`...`	Other arguments for `print`.

Details

Objects of class LinkedPairs are stored as square matrices of list elements with dimnames derived from the dimnames of the object of class ”Synteny” from which it was created. The diagonal of the matrix is only filled if OutputFormat ”Comprehensive” is selected in NucleotideOverlap, in which case it will be filled with the gene locations supplied to GeneCalls. The upper triangle is always filled, and contains location information in nucleotide space for all syntenic hits that link features between sequences in the form of an integer matrix with named columns. ”QueryGene” and ”SubjectGene” correspond to the integer rownames of the supplied gene calls. ”QueryIndex” and ”SubjectIndex” correspond to ”Index1” and ”Index2” columns of the source synteny object position. Remaining columns describe the exact positioning and size of extracted hits. The lower triangle is not filled if OutputFormat ”Sparse” is selected and contains relative displacement positions for the 'left-most' and 'right-most' hit involved in linking the particular features indicated in the related line up the corresponding position in the upper triangle.

The object serves only as a simple package for input data to the PairSummaries function, and as such may not be entirely user friendly. However it has been left exposed to the user should they find this data interesting.