Multi-omics data preprocessing

The section is designed for data preprocessing of raw omics data.

1. preprocess_omics_map2hic

For other omics data, they are first organized into bed format files.

dna.preprocess_omics_map2hic(multi_omics)

Arguments

Required arguments:

• multi_omics: Only accept ‘gene expression’, ‘nucleosome density’, and ‘histone marker’ currently. Other omics data can also be added if they have been appropriately prepared.

Data path

input data path: /in_data_folder/multi_omics

output data path: /out_data_folder/multi_omics/resolution/out_data

2. preprocess_omics_heatmap

Then, multi-omics datasets are mapped to the Hi-C adjacency matrices and heatmaps are drawn based on the genomic feature matrices.

dna.preprocess_omics_heatmap(multi_omics, type_of_calculation, fig_dpi = 300)

Arguments

Required arguments:

• multi_omics: Only accept ‘gene expression’, ‘nucleosome density’, and ‘histone marker’ currently. Other omics data can also be added if they have been appropriately prepared.

• type_of_calculation: Two options for the value of multi-omics data in the crossed window. It should be setted as ‘mean’ or ‘max’.

Optional arguments:

• fig_dpi: Figure resolution in dots per inch. The default is 300.

Data path

output data path: With the output of the previous function as input, the zscore matrix and heatmap are generated to /out_data_folder/multi_omics/resolution/out_plot.