pgLM-class: Class for reference based pangenome data

In thomasp85/FindMyFriends: Microbial Comparative Genomics in R

Description

This class handles pangenome information where gene sequences are kept on disc instead of stored in memory. As long as the original fasta files are not modified, this class will take care of indexing the genes correctly. This class has a substantially lower memory footprint than the pgFull class at the expense of longer sequence lookup times. For massive pangenomes containing Gb of sequence data there is no alternative though.

Slots

seqIndex

A data.frame as produced by fasta.index with random access information for each gene.

See Also

Other Pangenome_classes: pgFull-class, pgFullLoc-class, pgInMem-class, pgInMemLoc-class, pgLMLoc-class, pgSlim-class, pgSlimLoc-class, pgVirtual-class, pgVirtualLoc-class

thomasp85/FindMyFriends documentation built on April 25, 2020, 1:06 p.m.