Notebooks for analysis are contained in the notebook folder. Open folder and click on notebook
test data is in the data/test folder
Followed cookiecutter data science project template
basic prep for snp analysis
├── LICENSE
├── Makefile <- Makefile with commands like `make data` or `make train`
├── README.md <- The top-level README for developers using this project.
├── data
│ ├── external <- Data from third party sources.
│ ├── interim <- Intermediate data that has been transformed.
│ ├── processed <- The final, canonical data sets for modeling.
│ └── raw <- The original, immutable data dump.
│
├── docs <- A default Sphinx project; see sphinx-doc.org for details
│
├── models <- Trained and serialized models, model predictions, or model summaries
│
├── notebooks <- Jupyter notebooks. Naming convention is a number (for ordering),
│ the creator's initials, and a short `-` delimited description, e.g.
│ `1.0-jqp-initial-data-exploration`.
│
├── references <- Data dictionaries, manuals, and all other explanatory materials.
│
├── reports <- Generated analysis as HTML, PDF, LaTeX, etc.
│ └── figures <- Generated graphics and figures to be used in reporting
│
├── requirements.txt <- The requirements file for reproducing the analysis environment, e.g.
│ generated with `pip freeze > requirements.txt`
│
├── setup.py <- makes project pip installable (pip install -e .) so src can be imported
├── src <- Source code for use in this project.
│ ├── __init__.py <- Makes src a Python module
│ │
│ ├── data <- Scripts to download or generate data
│ │ └── make_dataset.py
│ │
│ ├── features <- Scripts to turn raw data into features for modeling
│ │ └── build_features.py
│ │
│ ├── models <- Scripts to train models and then use trained models to make
│ │ │ predictions
│ │ ├── predict_model.py
│ │ └── train_model.py
│ │
│ └── visualization <- Scripts to create exploratory and results oriented visualizations
│ └── visualize.py
│
└── tox.ini <- tox file with settings for running tox; see tox.readthedocs.io
Project based on the cookiecutter data science project template. #cookiecutterdatascience
Additional Information
How to interpret DNA strand and allele information for Infinium genotyping array data | Illumina Knowledge
Infinium Global Screening Array v3.0 Support Files (illumina.com)
ILMN Strand: The Top/Bot (for SNPs) or Plus/Minus (for Indels) designation of the ILMN strand (Design strand).
SNP: SNP alleles as reported by assay probes. Alleles on the Design strand (the ILMN strand) are listed in order of Allele A/B.
AddressA_ID: For Infinium I bead types, this is the Address ID for the probe specific for the A allele. For Infinium II bead types, the Address ID for the probe used for both A and B alleles (in this case, AddressB_ID and AlleleB_ProbeSeq columns are empty).
AlleleA_ProbeSeq: The sequence of the probe identified in AddressA_ID column.
AddressB_ID: For Infinium I bead types, the address ID for the probe specific for the B allele.
AlleleB_ProbeSeq: For Infinium I bead types, the sequence of the probe identified in AddressB_ID column.
GenomeBuild: The NCBI Genome Build referenced for information about this probe in this manifest.
Chr: Chromosome containing the SNP.
MapInfo: Chromosomal coordinates of the SNP.
Ploidy: Ploidy of the target organism. For humans, autosomes are diploid, mitochondria and Y chromosome are monoploid.
Species: Species targeted by the probes in this BeadArray.
Source: The database source of the SNP, if available (eg, dbSNP).
SourceVersion: The database (Source) version, if available, which was referenced for the SNP to create the manifest.
Source Strand: The Top/Bot (for SNPs) or Plus/Minus (for Indels) designation for the Source strand.
Source Seq: The sequence of the Source strand.
TopGenomicSeq (in *.csv version of manifest, but not in *.bpm): The sequence of the Top strand (for SNPs) or the Plus strand (for Indels).
BeadSetID: An identifier used in the manufacture of BeadChips.
Exp_Clusters: The number of clusters expected to be generated by each SNP: 1 for nonpolymorphic probes, 2 for mitochondrial DNA and Y chromosome loci, 3 for any other loci for a diploid organism.
Ref Strand: Plus/Minus (+/-) designation for the ILMN strand.