import_association_file: Import the association file from disk

In calabrialab/ISAnalytics: Analyze gene therapy vector insertion sites data identified from genomics next generation sequencing reads for clonal tracking studies

Import the association file from disk

Description

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. Use transformations instead.
...	Additional arguments to pass to import_Vispa2_stats

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)

Value

The data frame containing metadata

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)

calabrialab/ISAnalytics documentation built on Dec. 10, 2024, 10:50 p.m.