Real Data Analysis With coiaf

This repository stores the real data analysis conducted to test the software package {coiaf}.

Data Source

We analysed samples from the MalariaGEN Plasmodium falciparum Community Project [1]. The MalariaGEN Plasmodium falciparum Community Project provides genomic data from over 7,000 P. falciparum samples from 28 malaria-endemic countries in Africa, Asia, South America, and Oceania from 2002-2015. Detailed information about the data release including brief descriptions of contributing partner studies and study locations is available in the supplementary of MalariaGEN et al..

Project Structure

.
├── analysis
│   ├── estimation-comparison.Rmd
│   └── pf6_analysis.Rmd
├── data-outputs
│   ├── core-genome.rds
│   ├── data_dims.rds
│   ├── rmcl_estimation.rds
│   └── seq-error
│       ├── seq_0.01.rds
│       ├── seq_0.05.rds
│       ├── seq_0.1.rds
│       ├── seq_0.15.rds
│       └── seq_0.2.rds
├── download
│   ├── 00_Pf6_vcf_filtering.Rmd
│   ├── 01_create_coiaf_inputs.Rmd
│   ├── 02_run_rmcl.Rmd
│   └── core-genome.tsv
├── figures
│   ├── cluster-locations.png
│   ├── coi-world.png
│   ├── comparison.png
│   ├── continuous-region.png
│   ├── deploid.png
│   ├── discrete-region.png
│   ├── fws.png
│   ├── grouped-prevalence.png
│   ├── log-prevalence.png
│   ├── silhoutte.png
│   └── varying-seq-error.png
├── metadata
│   ├── deploidibd_data.rdata
│   ├── pf6_meta.Rmd
│   └── pf6_meta.rds
├── raw-regions
└── scripts
    ├── coi-region.R
    ├── combine-raw-regions.R
    ├── data-dimensions.R
    ├── rmcl-estimation.R
    └── slurm-region.R

References

1. MalariaGEN, Ahouidi A, Ali M, Almagro-Garcia J, Amambua-Ngwa A, Amaratunga C, et al. An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples. Wellcome Open Research. 2021;6: 42. doi:10.12688/wellcomeopenres.16168.1