Simulated exome-sequencing data for a family study of lymphoid cancer
Bibliographic record
Abstract
This repository contains all the data files for a simulated exome-sequencing study of 150 families, ascertained to contain at least four members affected with lymphoid cancer. Please note that previous versions of this repository omitted a key file linking the genotypes of individuals to their family and individual IDs; this file, geno_key.txt, is now included. All other files remain the same as in previous versions. The simulated data can be found in the files section below. The files are: SLiM_output.txt - contains the SLiM-simulated, exome-wide, SNV data generated under an American-admixture demographic model, for the American-admixed sub-population only. SLiM_output_chr8&9.txt - contains the SLiM-simulated data above for all source populations as well as the American-admixed sub-population, but only for chromosomes 8 and 9. sample_info.txt - contains pedigree information of all the disease-affected individuals and individuals connecting them along a line of descent, for all 150 ascertained pedigrees. Genotypes.zip - a zipfile that contains 22 text files of genotypes for each chromosome. The genotypes are for simulated single-nucleotide variants on the exome and are in gene-dosage format. geno_key.txt – a plain-text file that links the genotyped individuals to their family and individual IDs. SNVmaps.zip - a zipfile that contains 22 text files giving the single-nucleotide variant information for each chromosome. familial_cRV.txt - contains the familial causal rare variants for all 150 ascertained pedigrees. study_peds.txt - contains the 150 pedigrees ascertained to contain four or more relatives affected with lymphoid cancer. PLINKfiles.zip - a zipfile that contains PLINK .fam, .bim and .bed files for all 22 of the chromosomes. All the scripts used to generate these data can be found in the GitHub repository archived at https://zenodo.org/records/12694914 We have also uploaded one intermediate .Rdata file, Chromwide.Rdata, to save the user substantial time when running the associated RMarkdown script for the simulation. We recommend loading Chromwide.Rdata into your R work-space rather than generating it from scratch.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.002 | 0.009 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.002 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.002 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.102 | 0.031 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".