bioinf-proj

Methylation sites as a biomarker for cancer types - Bioinformatics project #4

Usage

main.py --help for the complete list of commands

usage: main.py [-h] [-cl2 | -cl3] [-svm | -knn | -rforest | -kmeans | -hierarc] [-over | -smote] [-ttest | -fisher | -anova | -pca | -lda | -sfs | -ga] [-d DOWNLOAD DOWNLOAD] [-ds DOWNLOADSANE DOWNLOADSANE] [-s STORE] [--alpha ALPHA] [--perc PERC] [-rs R_STATE] [--only_chrms_t] [--crossval] [--plot_lc] [--remove_nan_cpgs REMOVE_NAN_CPGS]

Bioinf project. The arguments can be passed in any order. The dataset MUST be unzipped in a directory called 'data'

optional arguments:

• -h, --help show this help message and exit
• -cl2 in order to classify two cancer types.
• -cl3 in order to classify two cancer types AND sane.
• -svm train a Support Vector Machine classifier
• -knn train a K Nearest Neighbors classifier
• -rforest train a Random Forest classifier
• -kmeans train a Kmeans clustering
• -hierarc train an Agglomerative Hierarchical clustering
• -over imbalance: Random Oversampling
• -smote imbalance: SMOTE
• -ttest feature selection: ttest per chromosoma and per cpg site - 2 classes
• -fisher feature selection: fisher criterion - 3 classes
• -anova feature selection: anova - 3 classes
• -pca dimensionality reduction: Principal Component Analisys
• -lda dimensionality reduction: Linear Discriminant Analysis
• -sfs feature selection - wrapper: Step Forward Selection (nearly unfeasible)
• -ga feature selection - wrapper: Genetic Algorithm
• -d DOWNLOAD DOWNLOAD, --download DOWNLOAD DOWNLOAD download Adenoma and Adenocarcinoma and Squamous Cell Neoplasm data from Genomic Data Common. It needs 2 parameters: first parameter is the destination folder; second parameters is the number of files to be downloaded for each class
• -ds DOWNLOADSANE DOWNLOADSANE, --downloadsane DOWNLOADSANE DOWNLOADSANE download Sane data from Genomic Data CommonIt needs 2 parameters: first parameter is the destination folder; second parameters is the number of files to be downloaded
• -s STORE, --store STORE concatenate files belonging to same cancer type and store them in a binary file
• --alpha ALPHA to set a different ALPHA: ttest parameter - default is 0.001
• --perc PERC to set PERC of varaince explained by the features kept by PCA
• -rs R_STATE, --r_state R_STATE to set a user defined Random State - default is 8
• --only_chrms_t select only chrms for ttest
• --crossval to do crossvalidation OR in case of unsupervised to plot the Inertia curve
• --plot_lc plot the learning curve
• --remove_nan_cpgs REMOVE_NAN_CPGS IF True: removes features containing at least one NaN value. IF False: NaN are substituted by the mean over the feature. The old file resulted by feature reduction must be eliminated when changing option. By Default is True.

Interesting GDC Queries

Adenomas and Adenocarcinomas

cases.disease_type in ["Adenomas and Adenocarcinomas"]
and cases.primary_site in ["Bronchus and lung"]
and files.data_category in ["DNA Methylation"]
and files.platform in ["Illumina Human Methylation 450"]
and cases.samples.sample_type in ["Primary Tumor","Recurrent Tumor"]

files*: 437

cases: 425

size: 61.73 GB

Squamous Cell Neoplasm

cases.disease_type in ["Squamous Cell Neoplasms"]
and cases.primary_site in ["Bronchus and lung"]
and files.data_category in ["DNA Methylation"]
and files.platform in ["Illumina Human Methylation 450"]
and cases.samples.sample_type in ["Primary Tumor","Recurrent Tumor"]

files: 370

cases: 372

size: 52.28 GB

Methylation Liftover Fields

• Composite Element: A unique ID for the array probe associated with a CpG site
• Beta Value: Represents the ratio between the methylated array intensity and total array intensity,
  falls between 0 (lower levels of methylation) and 1 (higher levels of methylation)
• Chromosome: The chromosome in which the probe binding site is located
• Start: The start of the CpG site on the chromosome
• End: The end of the CpG site on the chromosome
• Gene Symbol: The symbol for genes associated with the CpG site. Genes that fall within 1,500 bp upstream of the transcription start site (TSS) to the end of the gene body are used.
• Gene Type: A general classification for each gene (e.g. protein coding, miRNA, pseudogene)
• Transcript ID: Ensembl transcript IDs for each transcript associated with the genes detailed above
  *Position to TSS: Feature Type Distance in base pairs from the CpG site to each associated transcript’s start site
• CGI Coordinate: The start and end coordinates of the CpG island associated with the CpG site
• Feature Type: The position of the CpG site in reference to the island: Island, N_Shore or S_Shore (0-2 kb upstream or downstream from CGI), or N_Shelf or S_Shelf (2-4 kbp upstream or downstream from CGI)