Description Usage Arguments Value Examples
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.
1 | 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 |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | 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)
|
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