cell_structure_example: Example of cell types matching table

In tdw1221/NITUMID: Non-negative Matrix Factorization-based Immune-TUmor MIcroenvironment Deconvolution

Description

This is a dataframe that serves as reference when testing NITUMID's performance on datasets that with different cell types specification. For example, if you have a melanoma dataset with known cell types proportions for T cells, DC, Macrophages, Mature B cells (MB), NK cells and other cells together, then it does not match NITUMID's 11-celltype setup. In this case, you could use this dataframe to specify the matching relationships between your known cell types and NITUMID's cell types. This dataframe has two column, 'origina_index' marks our 11 cell types from 1 to 11, you are not supposed to modify that; you can modify 'destin_index' accordingly as DC-1, CD4-2, CD8-2, Macrophages-3, MB-4, NK-5, Monocytes-6, Plasma-6, MAST-6, Eosinophil-6, Melanoma-6. Basically, we merged CD4+ T cell and CD8+ T cell into one cell type, and all our cell types after monocytes into the 6-th cell type.

origina_index

Indexed NITUMID's 11 cell types, from 1 to 11

destin_index

Indexed customized cell types

tdw1221/NITUMID documentation built on May 31, 2019, 1:54 a.m.