epitoolkit 0.2.6

EpiToolkit is a set of tools useful in the analysis of data from EPIC / 450K microarrays.

EpiGenToolKit

Is a small library created to deal with data from EPIC / 450K microarrays. The tool allows to:

a) Simply visualize methylation levels of specific CpG or genomic region.

b) Perform enrichment analysis of a selected subset of CpG against the whole array. In this type of analysis expected frequency [%] (based on mynorm) of genomic regions is compared to observed (based on provided cpgs set), results are comapred using chi-square test.

How to start?

a) using env

python -m venv env
source env/bin/activate # Windows: env\Scripts\activate
pip install epitoolkit

b) using poetry

poetry new .
poetry add epitoolkit

c) or just clone the repository:

git clone https://github.com/ClinicalEpigeneticsLaboratory/EpiGenToolKit.git
cd EpiGenToolKit && poetry install

How to use?

Visualization

To visualize single CpG site or specific genomic region initialize Visualise object:

from epitoolkit.tools import Visualize

viz = Visualize(manifest=<path_to_array_manifest>, # path to manifest file
                mynorm=<path_to_mynorm_file>, # path to mynorm file
                poi=<path_to_poi_file>, # path to poi file
                poi_col=<column_name> # name of column containing sample phenotype
                skiprows=0) # many manifest contains headers, set skiprows argument to ignore them.

all files must have *.csv extension, mynorm must contain sample names as columns and cpgs as rows, the proper EPIC manifest may be downloaded from here, poi file must contain sample names rows (only samples overlapped between poi and mynorm will be used) and POI (phenotype of interest) column containing names of phenotype e.g. Control and Case.

To visualize single CpG:

viz.plot_CpG("cg07881041", # cpg ID
    static=False, # plot type static / interactive [default]
    height=400, # plot size [default]
    width=700, # plot size [default]
    title="", # plot title [default]
    legend_title="", # legend title [default]
    font_size=22, # font size [default]
    show_legend=True, # False to hide legedn [default]
    x_axis_label="CpG", # x axsis label [default]
    category_order=["Cohort 1", "Cohort 2], # box order [default]
    y_axis_label="beta-values") # y axis label [default]

NOTE: most of those arguments are default! So you don't need to specify most of them!

To visualize specific genomic region:

vis.plot_Range(chr=17, start=5999, end=7000)

NOTE: please note that all arguments available in viz.plot_CpG are also in plot_Range

To visualize specific CpGs in genomic order, instead of whole region, just pass collection of CpGs:

viz.plot_Range(cpgs=["cg04594855", "cg19812938", "cg05451842"]

To save plots use export argument, for instance:

viz.plot_Range(chr=17, start=5999, end=6770, export="plot.html") # if static = False only html format is supported if static = True, use png extension.

Enrichment analysis

To perform enrichment analysis against any type of genomic region specified in the manifest file, the user needs to initialize EnrichemntAnalysis object.

from src.epitoolkit.tools import EnrichmentAnalysis

ea = EnrichmentAnalysis(manifest=<path_to_array_manifest>,
        mynorm=<path_to_mynorm_file>)

or if Visualize object already exists use load method (this approach makes you not have to load the data again):

ea = EnrichmentAnalysis.load(<Visualize_object_name>)

To start analysis:

ea.enrichmentAnalysis(categories_to_analyse=["UCSC_RefGene_Group", "Relation_to_UCSC_CpG_Island"],  # list of categories to analyse
                cpgs=cpgs) # list of cpgs to analyse against background