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Import the association file from disk

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

[Stable] Imports the association file and optionally performs a check on the file system starting from the root to assess the alignment between the two.

Usage

import_association_file(
  path,
  root = NULL,
  dates_format = "ymd",
  separator = "\t",
  filter_for = NULL,
  import_iss = FALSE,
  convert_tp = TRUE,
  report_path = default_report_path(),
  transformations = default_af_transform(convert_tp),
  tp_padding = lifecycle::deprecated(),
  ...
)

Arguments

path

The path on disk to the association file.

root

The path on disk of the root folder of VISPA2 output or NULL. See details.

dates_format

A single string indicating how dates should be parsed. Must be a value in: date_formats()

separator

The column separator used in the file

filter_for

A named list where names represent column names that must be filtered. For example: list(ProjectID = c("PROJECT1", "PROJECT2)) will filter the association file so that it contains only those rows for which the value of the column "ProjectID" is one of the specified values. If multiple columns are present in the list all filtering conditions are applied as a logical AND.

import_iss

Import VISPA2 pool stats and merge them with the association file? Logical value

convert_tp

Should be time points be converted into months and years? Logical value

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.

transformations

Either NULL or a named list of purrr-style lambdas where names are column names the function should be applied to.

tp_padding

[Deprecated] Deprecated. Use transformations instead.

...

Additional arguments to pass to import_Vispa2_stats

Value

The data frame containing metadata

Details

Transformations

Lambdas provided in input in the transformations argument, must be transformations, aka functions that take in input a vector and return a vector of the same length as the input.

If the transformation list contains column names that are not present in the data frame, they are simply ignored.

File system alignment

If the root argument is set to NULL no file system alignment is performed. This allows to import the basic file but it won't be possible to perform automated matrix and stats import. For more details see the "How to use import functions" vignette: vignette("workflow_start", package = "ISAnalytics")

Time point conversion

The time point conversion is based on the following logic, given TPD is the column containing the time point expressed in days and TPM and TPY are respectively the time points expressed as month and years

  • If TPD is NA --> NA (for both months and years)

  • TPM = 0, TPY = 0 if and only if TPD = 0

For conversion in months:

  • TPM = ceiling(TPD/30) if TPD < 30 otherwise TPM = round(TPD/30)

For conversion in years:

  • TPY = ceiling(TPD/360)

Required tags

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

  • project_id

  • pool_id

  • tag_seq

  • subject

  • tissue

  • tp_days

  • cell_marker

  • pcr_replicate

  • vispa_concatenate

  • pcr_repl_id

  • proj_folder

The function will use all the available specifications contained in association_file_columns(TRUE) to read and parse the file. If the specifications contain columns with a type "date", the function will parse the generic date with the format in the dates_format argument.

See also

transform_columns

date_formats

Other Import functions: import_Vispa2_stats(), 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,
    report_path = NULL
)
head(af)
#> # A tibble: 6 × 74
#>   ProjectID FUSIONID  PoolID TagSequence SubjectID VectorType VectorID
#>   <chr>     <chr>     <chr>  <chr>       <chr>     <chr>      <chr>   
#> 1 PJ01      ET#382.46 POOL01 LTR75LC38   PT001     lenti      GLOBE   
#> 2 PJ01      ET#381.40 POOL01 LTR53LC32   PT001     lenti      GLOBE   
#> 3 PJ01      ET#381.9  POOL01 LTR83LC66   PT001     lenti      GLOBE   
#> 4 PJ01      ET#381.71 POOL01 LTR27LC94   PT001     lenti      GLOBE   
#> 5 PJ01      ET#381.2  POOL01 LTR69LC52   PT001     lenti      GLOBE   
#> 6 PJ01      ET#382.28 POOL01 LTR37LC2    PT001     lenti      GLOBE   
#> # ℹ 67 more variables: ExperimentID <chr>, Tissue <chr>, TimePoint <chr>,
#> #   DNAFragmentation <chr>, PCRMethod <chr>, TagIDextended <chr>,
#> #   Keywords <chr>, CellMarker <chr>, TagID <chr>, NGSProvider <chr>,
#> #   NGSTechnology <chr>, ConverrtedFilesDir <chr>, ConverrtedFilesName <chr>,
#> #   SourceFileFolder <chr>, SourceFileNameR1 <chr>, SourceFileNameR2 <chr>,
#> #   DNAnumber <chr>, ReplicateNumber <int>, DNAextractionDate <date>,
#> #   DNAngUsed <dbl>, LinearPCRID <chr>, LinearPCRDate <date>, …