Bamtools file parsing and manipulation.
Methods
Inherited methods
Method new()
Create a new Bamtools object.
Usage
Bamtools$new(path = NULL, files_tbl = NULL)
Arguments
path(character(1))
Output directory of tool. If files_tbl is supplied, this basically gets
ignored.
files_tbl(tibble(n))
Tibble of files from list_files_dir.
Method parse_summary()
Read summary.tsv file.
Usage
Bamtools$parse_summary(x)
Arguments
x(character(1))
Path to file.
Method tidy_summary()
Tidy summary.tsv file.
Arguments
x(character(1))
Path to file.
Method parse_wgsmetrics()
Read wgsmetrics file.
Usage
Bamtools$parse_wgsmetrics(x)
Arguments
x(character(1))
Path to file.
Method tidy_wgsmetrics()
Tidy wgsmetrics file.
Usage
Bamtools$tidy_wgsmetrics(x)
Arguments
x(character(1))
Path to file.
Method parse_flagstats()
Read flag_counts.tsv file.
Usage
Bamtools$parse_flagstats(x)
Arguments
x(character(1))
Path to file.
Method tidy_flagstats()
Tidy flag_counts.tsv file.
Usage
Bamtools$tidy_flagstats(x)
Arguments
x(character(1))
Path to file.
Method parse_coverage()
Read coverage.tsv file.
Usage
Bamtools$parse_coverage(x)
Arguments
x(character(1))
Path to file.
Method tidy_coverage()
Tidy coverage.tsv file.
Usage
Bamtools$tidy_coverage(x)
Arguments
x(character(1))
Path to file.
Method parse_fraglength()
Read frag_length.tsv file.
Usage
Bamtools$parse_fraglength(x)
Arguments
x(character(1))
Path to file.
Method tidy_fraglength()
Tidy frag_length.tsv file.
Usage
Bamtools$tidy_fraglength(x)
Arguments
x(character(1))
Path to file.
Method parse_partitionstats()
Read partition_stats.tsv file.
Usage
Bamtools$parse_partitionstats(x)
Arguments
x(character(1))
Path to file.
Method tidy_partitionstats()
Tidy partition_stats.tsv file.
Usage
Bamtools$tidy_partitionstats(x)
Arguments
x(character(1))
Path to file.
Method clone()
The objects of this class are cloneable with this method.
Usage
Bamtools$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
Examples
if (FALSE) { # \dontrun{
path <- here::here("nogit")
b <- Bamtools$new(path)
} # }