pangenome {FindMyFriends} | R Documentation |
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.
pangenome(paths, translated, geneLocation = NULL, lowMem = FALSE, ...)
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 |
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 |
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)