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Documentation for 'get_livertobw_score' Function

Md Aminul Islam Prodhan

2025-01-02

Source: vignettes/get_livertobw_score.Rmd
get_livertobw_score.Rmd

Purpose

The get_livertobw_score function is designed to calculate liver-to-body-weight (LiverToBW) ratio and their corresponding z-scores from study data. This function supports data retrieval from SQLite databases or .xpt files and provides options to return individual scores, USUBJID-specific z-scores, or averaged scores by study. The weight of each animal at the end of the dosing period was normalized by subtracting the baseline weight measured on the first day of dosing. Following this, the liver weight to body weight ratio was calculated for each animal. These liver-to-body weight ratios were then normalized using Z-scores, with comparisons made against the respective control group for each study

Function Parameters (Arguments)

Inputs

Parameter Type Default Description
studyid character NULL The STUDYID of the study for which the BW score is to be calculated. Required when use_xpt_file = FALSE. If use_xpt_file = TRUE, studyid is ignored, and the .xpt files of that study in the specified folder are analyzed.
path_db character N/A Path to the SQLite database or .xpt files.
fake_study logical FALSE Indicator for handling fake or test study data.
use_xpt_file logical FALSE If TRUE, reads data from .xpt files. Otherwise, fetches data from the SQLite database.
master_compiledata data.frame NULL If master_compiledata is not supplied (i.e., NULL) , it is fetched using get_compile_data().
bwzscore_BW data.frame NULL If bwzscore_BW is not supplied (i.e., NULL),it is fetched using using get_bw_score().
return_individual_scores logical FALSE If TRUE, returns averaged z-score for each domain calculated from the scores of all subjects/animals (USUBJID).
return_zscore_by_USUBJID logical FALSE If TRUE, returns Z-scores for each animal/subject (identified by USUBJID).

Key Points: - Mandatory Parameter: path_db is required for the function to work. - Logical Exclusivity: Both return_individual_scores and return_zscore_by_USUBJID cannot be TRUE simultaneously.

Outputs

A data.frame containing the calculated LiverToBW Z-scores. The structure of the output depends on the provided parameters:

  • If return_individual_scores = TRUE: Returns averaged Z-scores for each of the domain per studyid.
  • If return_zscore_by_USUBJID = TRUE: Returns Z-score for each animal/subject by USUBJID for each domain per studyid.
  • Otherwise, a summarized BW Z-score for the specified studyid.

Implementation Details

Data Preparation

  • Database Connection:
    • Connects to SQLite database using DBI if use_xpt_file = FALSE.
    • If use_xpt_file = TRUE: Data is loaded from .xpt files located in the folder specified by path_db.
  • Compile Data:
  • Body Weight Scores:
    • If bwzscore_BW is not supplied, it is calculated using get_bw_score().

Data Retrieval

The function retrieves the necessary data related to the specified studyid. The data retrieval process depends on whether master_compiledata is provided or NULL:

When master_compiledata = NULL,

If master_compiledata is not provided, the function extracts data from the following SEND domains:

  • BW (Body Weight) : Provide the Body Weight measurements at the individual level.
  • DM (Demographics): Supplies animal-level demographic details.
  • DS (Disposition): Identifies recovery animals using the DSDECOD column.
  • PC (Pharmacokinetics): Provide USUBJID of the TK animals for rats and mice study.
  • TX (Treatment): Provide dose levels information such as “vehicle” or “HD.”

When master_compiledata is Provided,

If master_compiledata value is provided, this function retrieve the following domains:

  • OM (Organ Measurements) : Provide the Organ measurements at the individual level.

Liver-to-Body-Weight Calculations

  • Calculation:
    • Computes the liver weight-to-body-weight ratio (liverToBW).
    • Calculates z-scores for liverToBW using vehicle arm statistics (mean and SD).
    • Converts z-scores to absolute values.

Handling Optional Parameters

  • If return_individual_scores = TRUE, Returns averaged Z-scores for each of the domain per studyid.
  • If return_zscore_by_USUBJID = TRUE, Returns Z-score for each animal/subject by unique subject identifiersUSUBJID.

Fake Study Handling

If fake_study = TRUE, special handling is applied for data sets generated by the SENDsanitizer package to account for their structure.

Output Generation

A data frame containing the requested scores is returned. This may include summarized scores, individual scores, or Z-scores by USUBJID, based on the parameters provided.

Dependencies

The function requires the following R packages:

  • RSQLite: To connect to the SQLite database.
  • haven : To read .xpt file, if use_xpt_file = TRUE.

This implementation ensures flexibility in handling different input types and configurations while maintaining a consistent structure for the output.

Examples

Example 1: Default Averaged Scores

```r #path <- “path_to_database” #study_id <- “STUDY123” #result <- get_livertobw_score(studyid = study_id, path_db = path) #head(result)