Bamtools Object

Bamtools file parsing and manipulation.

Super class

nemo::Tool -> Bamtools

Methods

Public methods

• Bamtools$new()

• Bamtools$parse_summary()

• Bamtools$tidy_summary()

• Bamtools$parse_wgsmetrics()

• Bamtools$tidy_wgsmetrics()

• Bamtools$parse_flagstats()

• Bamtools$tidy_flagstats()

• Bamtools$tidy_genecvg()

Inherited methods

• nemo::Tool$filter_files()
• nemo::Tool$get_metadata()
• nemo::Tool$get_tbls()
• nemo::Tool$list_files()
• nemo::Tool$print()
• nemo::Tool$run()
• nemo::Tool$tidy()
• nemo::Tool$write()

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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 is ignored.

files_tbl

(tibble(n))
Tibble of files from nemo::list_files_dir().

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Method parse_summary()

Read summary.tsv file.

Usage

Bamtools$parse_summary(x)

Arguments

x

(character(1))
Path to file.

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Method tidy_summary()

Tidy summary.tsv file. Generates 2 sub-tbls: stats with the main stats and dp with the percentage of bases covered by at least X reads.

Usage

Bamtools$tidy_summary(x)

Arguments

x

(character(1))
Path to file.

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Method parse_wgsmetrics()

Read wgsmetrics file.

Usage

Bamtools$parse_wgsmetrics(x)

Arguments

x

(character(1))
Path to file.

---

Method tidy_wgsmetrics()

Tidy wgsmetrics file. Generates 3 sub-tbls: stats with the main stats, dp with the percentage of bases covered by at least X reads, and histo with the distribution of base coverage.

Usage

Bamtools$tidy_wgsmetrics(x)

Arguments

x

(character(1))
Path to file.

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Method parse_flagstats()

Read flag_counts.tsv file.

Usage

Bamtools$parse_flagstats(x)

Arguments

x

(character(1))
Path to file.

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Method tidy_flagstats()

Tidy flag_counts.tsv file.

Usage

Bamtools$tidy_flagstats(x)

Arguments

x

(character(1))
Path to file.

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Method tidy_genecvg()

Tidy gene_coverage.tsv file.

Usage

Bamtools$tidy_genecvg(x)

Arguments

x

(character(1))
Path to file.

Examples

cls <- Bamtools
indir <- system.file("extdata/oa", package = "tidywigits")
odir <- tempdir()
id <- "bamtools_run1"
obj <- cls$new(indir)
obj$run(output_dir = odir, format = "parquet", input_id = id)
(lf <- list.files(odir, pattern = "bamtools_.*parquet", full.names = FALSE))
#>  [1] "sample1_2_bamtools_flagstats.parquet"    
#>  [2] "sample1_bamtools_coverage.parquet"       
#>  [3] "sample1_bamtools_exoncvg.parquet"        
#>  [4] "sample1_bamtools_flagstats.parquet"      
#>  [5] "sample1_bamtools_fraglength.parquet"     
#>  [6] "sample1_bamtools_genecvgcvg.parquet"     
#>  [7] "sample1_bamtools_genecvggenes.parquet"   
#>  [8] "sample1_bamtools_partitionstats.parquet" 
#>  [9] "sample1_bamtools_summarydp.parquet"      
#> [10] "sample1_bamtools_summarystats.parquet"   
#> [11] "sample1_bamtools_wgsmetricsdp.parquet"   
#> [12] "sample1_bamtools_wgsmetricshisto.parquet"
#> [13] "sample1_bamtools_wgsmetricsstats.parquet"