geneLocation

geneLocation,pgInMemLoc-method

object


This method returns the gene location of all genes as a data.frame with each
row corresponding to a gene in the pangenome. The data.frame will have the 
columns 'start', 'end', 'contig' and 'strand' (order of columns not ensured)
with start and end giving the start and end position of the gene on the 
contig/chromosome given in the contig column. Strand gives the direction of
translation, 1 is from start to end and -1 is from end to start (thus start 
should always be lower than end no matter the direction of translation)


A framework for doing microbial comparative genomics in R.
The main purpose of the package is assisting in the creation of
pangenome matrices where genes from related organisms are
grouped by similarity, as well as the analysis of these data.
FindMyFriends provides many novel approaches to doing pangenome
analysis and supports a gene grouping algorithm that scales
linearly, thus making the creation of huge pangenomes feasible.

Thomas Pedersen

FindMyFriends

Microbial Comparative Genomics in R

geneLocation function

<ul>
<li> <code>pgInMemLoc</code>: Get gene location for pgInMemLoc subclasses
</li>
</ul>

Methods (by class)

This method returns the gene location of all genes as a data.frame with each
row corresponding to a gene in the pangenome. The data.frame will have the 
columns 'start', 'end', 'contig' and 'strand' (order of columns not ensured)
with start and end giving the start and end position of the gene on the 
contig/chromosome given in the contig column. Strand gives the direction of
translation, 1 is from start to end and -1 is from end to start (thus start 
should always be lower than end no matter the direction of translation)

geneLocation: Get gene location for all genes

Description

Usage

Arguments

Value

Methods (by class)

Examples