pangenome: Construct a pangenome from fasta files

In thomasp85/FindMyFriends: Microbial Comparative Genomics in R

Description

This function constructs an initial pangenome object from a set of fasta files. Note that the actual pangenome is not calculated here. As such this function mainly sets everything up before beginning the more lengthly pangenome calculation.

Usage

pangenome(paths, translated, geneLocation = NULL, lowMem = FALSE, ...)

Arguments

paths	A character vector with location of fasta files
translated	A boolean indicating if the fasta files contain amino acid sequences
geneLocation	A function, string or dataframe. If it is a data.frame it should contain the columns 'contig', 'start', 'end' and 'strand' with a row for each gene. If it is a function it should take the name (fasta description) for each gene and output a data.frame similar to described above. If it is a string it should specify the format of the gene names. Currently only 'prodigal' is supported.
lowMem	Boolean. Should FindMyFriends avoid storing sequences in memory.
...	Additional defaults to set on the object

Value

A pgVirtual subclass object depending on geneLocation and lowMem.

geneLocation	lowMem	Resulting class
NULL	FALSE	pgFull
NULL	TRUE	pgLM
!NULL	FALSE	pgFullLoc
!NULL	TRUE	pgLMLoc

Examples

location <- tempdir()
unzip(system.file('extdata', 'Mycoplasma.zip', package='FindMyFriends'),
      exdir=location)
genomeFiles <- list.files(location, full.names=TRUE, pattern='*.fasta')

# Create pgFull
pangenome(genomeFiles, TRUE)

# Create pgFullLoc
pangenome(genomeFiles, TRUE, geneLocation='prodigal')

# Create pgLM
pangenome(genomeFiles, TRUE, lowMem=TRUE)

# Create pgLMLoc
pangenome(genomeFiles, TRUE, geneLocation='prodigal', lowMem=TRUE)

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