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Cross-talk gene classification analysis

gene_classification.Rd

The function calculates (saturation of) cross-talk diversity and (saturation of) interaction diversity involved in provided cross-talks

Usage

gene_classification(gs_ct = NULL, A = NULL, ct_ref = NULL, n_cores = 1)

Arguments

gs_ct

the data.frame obtained as a result of `gs_cross_talk()`, filtered if needed

A

the adjacency matrix used as an input in `gs_cross_talk()`

ct_ref

=`NULL` or a data.frame with cross-talk calculated on a reference. If provided, saturation `r_g` and `r_d` are calculated.

n_cores

number of cores to be use to parallelize gene gene set relevance analysis

Value

If `ct_ref = NULL` The function returns a data.frame with:

  • gene: the gene analysed

  • d_q: number of altered cross-talk `gene` contributes to

  • d_d: number of interactors contributing to any altered cross-talk together with `gene`

  • d_q_S: list of names of the gene-sets counted in `d_q` separated by `;`

  • d_d_gene: list of names of the genes counted in `d_d` separated by `;`

Otherwise, if `ct_ref` is provided the function returns a data.frame with:

  • gene: the gene analysed

  • d_q: cross-talk diversity, or number of gene set in altered cross-talk that contains interactors of `gene`

  • d_d: interaction diversity, or number of interactors of `gene` that are part of altered cross-talks

  • r_q: saturation of cross-talk diversity

  • r_d: saturation of interaction diversity

  • d_q_S: list of gene set names counted in `d_q` separated by `;`

  • d_d_gene: list of names of the genes counted in `d_d` separated by `;`

  • q: number of gene set in cross-talk that contains interactors of `gene`

  • d: number of interactors of `gene` that are part of cross-talks

  • q_S: list of gene set names counted in `q` separated by `;`

  • d_gene: list of names of the genes counted in `d` separated by `;`

Details

The function takes as an input the data.frame obtained from `gs_cross_talk()` and the adjacency matrix used as an input of `gs_cross_talk()`. These inputs are used to calculate (saturation of) cross-talk diversity and (saturation of) interaction diversity involved in significant cross-talks, as defined in the paper. This function has two applications:

  1. calculate cross-talk diversity and interaction diversity in a reference model

  2. calculate saturation of cross-talk diversity and saturation of interaction diversity by using the reference obtained in `1`