Amber file parsing and manipulation.
Methods
Inherited methods
Method new()
Create a new Amber object.
Usage
Amber$new(path = NULL, files_tbl = NULL)
Arguments
path(character(1))
Output directory of tool. If files_tbl is supplied, this basically gets
ignored.
files_tbl(tibble(n))
Tibble of files from nemo::list_files_dir().
Method parse_bafpcf()
Read baf.pcf file.
Arguments
x(character(1))
Path to file.
Method tidy_bafpcf()
Tidy baf.pcf file.
Arguments
x(character(1))
Path to file.
Method parse_baftsv()
Read baf.tsv.gz file.
Arguments
x(character(1))
Path to file.
Method tidy_baftsv()
Tidy baf.tsv.gz file.
Arguments
x(character(1))
Path to file.
Method parse_contaminationtsv()
Read contamination.tsv file.
Usage
Amber$parse_contaminationtsv(x)
Arguments
x(character(1))
Path to file.
Method tidy_contaminationtsv()
Tidy contamination.tsv file.
Usage
Amber$tidy_contaminationtsv(x)
Arguments
x(character(1))
Path to file.
Method parse_homozygousregion()
Read homozygousregion.tsv file.
Usage
Amber$parse_homozygousregion(x)
Arguments
x(character(1))
Path to file.
Method tidy_homozygousregion()
Tidy homozygousregion.tsv file.
Usage
Amber$tidy_homozygousregion(x)
Arguments
x(character(1))
Path to file.
Method parse_qc()
Read qc file.
Arguments
x(character(1))
Path to file.
Method tidy_qc()
Tidy qc file.
Arguments
x(character(1))
Path to file.
Method clone()
The objects of this class are cloneable with this method.
Usage
Amber$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
Examples
cls <- Amber
indir <- system.file("extdata/oa", package = "tidywigits")
odir <- tempdir()
id <- "amber_run1"
obj <- cls$new(indir)
obj$nemofy(odir = odir, format = "parquet", id = id)
#> NULL
(lf <- list.files(odir, pattern = "amber.*parquet", full.names = FALSE))
#> character(0)
