inst/markdown/extracellular_network_main.markdown

In CRI-iAtlas/iatlas-app: What the Package Does (One Line, Title Case)

Select the subset of interest of analysis, depending on the Sample Group selected. The additional parameters required to build a network are:

• Abundance threshold (%): Nodes in the network are selected if they meet the selected abundance threshold. The abundance threshold, in %, is the frequency of samples in the upper two tertiles of cell abundance or gene expression distributions. For example, for an abundance of 66%, a node (cell or gene) is entered into the subtype-network if at least 66% of samples within a subtype map to mid or high value bins in a tertile distribution of this node across all samples.

• Concordance threshold: Edges in the scaffold network between any two abundant nodes is evaluated for inclusion based on the selected concordance threshold. The concordance threshold is computed based on the contingency table populated with the ternary values of the two nodes of an edge and in terms of the values of ((high,high)+ (low,low))/(1+(low,high)+(high,low)). A concordance threshold of 2, for example, selects edges that have both nodes simultaneously highly or lowly expressed (concordant) at least twice as frequent than samples with one node highly expressed and the other lowly expressed (discordant). On the other hand, an edge with a concordance score of 0.5 is considered discordant, i.e., samples with one node highly expressed and the other lowly expressed (discordant) are twice as frequent than samples with both nodes simultaneously highly or lowly expressed (concordant).

In addition, a user can also select a set of cells or genes of interest. This selection will limit the network to the edges in the scaffold with the selected cells and genes that meet the abundance and concordance thresholds. By default, if there is no selection, a network will use all cells and immunomodulator genes (as described in the Immunomodulators module).

Manuscript context: This module allows you to display networks similar to Figure 7A, 7B, 7C, and S7A. Figure 7C can be generated by the following parameters selection:

In the CG Cohort Selection: - Select Datasets: TCGA - Select or Search for Grouping Variables: Immune Subtype

In this module: - Select Sample Groups: Immune Subtype - Select Immune Subtype: select all - Set Abundance Threshold (%): 66.6 - Set Concordance Threshold: 0 - Select cells of interest (optional): T cells CD4 and T cells CD8 - Hit "GO" - You may find that changing the layout (in Select Layout) to "concentric" improves the visualization of this network.

If you are still looking at Immune Subtypes, select Immune Subtype C4, 66% abundance threshold, 1.62 for concordance score, and leave the selection of cells and genes in blank to get the extracellular network for C4 present in Figure S7A.

CRI-iAtlas/iatlas-app documentation built on Feb. 7, 2025, 9:02 p.m.