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Import Vispa2 stats given the aligned association file.

Source: R/import-functions.R
import_Vispa2_stats.Rd

[Stable] Imports all the Vispa2 stats files for each pool provided the association file has been aligned with the file system (see import_association_file).

Usage

import_Vispa2_stats(
  association_file,
  file_prefixes = default_iss_file_prefixes(),
  join_with_af = TRUE,
  pool_col = "concatenatePoolIDSeqRun",
  report_path = default_report_path()
)

Arguments

association_file

The file system aligned association file (contains columns with absolute paths to the 'iss' folder)

file_prefixes

A character vector with known file prefixes to match on file names. NOTE: the elements represent regular expressions. For defaults see default_iss_file_prefixes.

join_with_af

Logical, if TRUE the imported stats files will be merged with the association file, if FALSE a single data frame holding only the stats will be returned.

pool_col

A single string. What is the name of the pool column used in the Vispa2 run? This will be used as a key to perform a join operation with the stats files POOL column.

report_path

The path where the report file should be saved. Can be a folder or NULL if no report should be produced. Defaults to {user_home}/ISAnalytics_reports.

Value

A data frame

Required tags

The function will explicitly check for the presence of these tags:

  • project_id

  • tag_seq

  • vispa_concatenate

  • pcr_repl_id

See also

Other Import functions: import_association_file(), import_parallel_Vispa2Matrices(), import_single_Vispa2Matrix()

Examples

fs_path <- generate_default_folder_structure(type = "correct")
af <- import_association_file(fs_path$af,
    root = fs_path$root,
    import_iss = FALSE,
    report_path = NULL
)
stats_files <- import_Vispa2_stats(af,
    join_with_af = FALSE,
    report_path = NULL
)
head(stats_files)
#> # A tibble: 6 × 14
#>   POOL     TAG       RUN_NAME     PHIX_MAPPING PLASMID_MAPPED_BYPOOL BARCODE_MUX
#>   <chr>    <chr>     <chr>               <dbl>                 <dbl>       <dbl>
#> 1 POOL01-1 LTR75LC38 PJ01|POOL01…     43586699               2256176      645026
#> 2 POOL01-1 LTR53LC32 PJ01|POOL01…     43586699               2256176      652208
#> 3 POOL01-1 LTR83LC66 PJ01|POOL01…     43586699               2256176      451519
#> 4 POOL01-1 LTR27LC94 PJ01|POOL01…     43586699               2256176      426500
#> 5 POOL01-1 LTR69LC52 PJ01|POOL01…     43586699               2256176       18300
#> 6 POOL01-1 LTR37LC2  PJ01|POOL01…     43586699               2256176      729327
#> # ℹ 8 more variables: LTR_IDENTIFIED <dbl>, TRIMMING_FINAL_LTRLC <dbl>,
#> #   LV_MAPPED <dbl>, BWA_MAPPED_OVERALL <dbl>, ISS_MAPPED_OVERALL <dbl>,
#> #   RAW_READS <lgl>, QUALITY_PASSED <lgl>, ISS_MAPPED_PP <lgl>