Peach file parsing and manipulation.
Methods
Inherited methods
Method new()
Create a new Peach object.
Usage
Peach$new(path = NULL, files_tbl = NULL)
Arguments
path(character(1))
Output directory of tool. If files_tbl is supplied, this basically gets
ignored.
files_tbl(tibble(n))
Tibble of files from nemo::list_files_dir().
Method parse_events()
Read events.tsv file.
Arguments
x(character(1))
Path to file.
Method tidy_events()
Tidy events.tsv file.
Arguments
x(character(1))
Path to file.
Method parse_eventsg()
Read gene.events.tsv file.
Arguments
x(character(1))
Path to file.
Method tidy_eventsg()
Tidy gene.events.tsv file.
Arguments
x(character(1))
Path to file.
Method parse_hapall()
Read haplotypes.all.tsv file.
Arguments
x(character(1))
Path to file.
Method tidy_hapall()
Tidy haplotypes.all.tsv file.
Arguments
x(character(1))
Path to file.
Method parse_hapbest()
Read haplotypes.best.tsv file.
Arguments
x(character(1))
Path to file.
Method tidy_hapbest()
Tidy haplotypes.best.tsv file.
Arguments
x(character(1))
Path to file.
Method parse_qc()
Read qc.tsv file.
Arguments
x(character(1))
Path to file.
Method tidy_qc()
Tidy qc.tsv file.
Arguments
x(character(1))
Path to file.
Method clone()
The objects of this class are cloneable with this method.
Usage
Peach$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
Examples
cls <- Peach
indir <- system.file("extdata/oa", package = "tidywigits")
odir <- tempdir()
id <- "peach_run1"
obj <- cls$new(indir)
obj$nemofy(diro = odir, format = "parquet", input_id = id)
#> NULL
(lf <- list.files(odir, pattern = "peach.*parquet", full.names = FALSE))
#> character(0)
