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Integrated cellular cross talk analysis

integrated_cross_talk.Rd

The function is a wrapper of `single_integrated_cross_talk()` and calculates inter-intracellular communication on multiple clusters.

Usage

integrated_cross_talk(
  cl_list,
  ccc_list,
  gs_list,
  A,
  k = 9,
  bin_type = "number",
  perm_link = "degree",
  perm_weights = "degree",
  cut_par = 3,
  mc_cores_perm = 1,
  mc_cores_ct = 1
)

Arguments

cl_list

cluster list used for communication analysis (provided as `S_list` to `gs_cross_talk()`)

ccc_list

communication details between cluster of interest

gs_list

list of gene set lists, one for each cluster considered in the analysis

A

adjacency matrix of the whole gene network considered (can be a sparseMatrix)

k

number of permutations

bin_type

can be either "number" (suggested), "interval" or "width". See `ggplot2::cut_interval()` for details.

perm_link

= c("degree", "simple") If the permutation of the link should be degree-conservative ("degree"), or random ("simple")

perm_weights

= c("degree", "simple") If the permutation of the weights should be degree-conservative ("degree"), or random ("simple")

cut_par

number of bin to cut. If set to `NULL`, the function will search for the best cut in 2:15

mc_cores_perm

number of thread to be used in permutations

mc_cores_ct

number of threads to be used for cross talk calculation

Value

The function returns a data.frame with the result of inter-intracellular communication:

  • ccc: cluster pair considered for integrated cross-talk analysis

  • S1_name,S2_name: names of gene-set pairs considered

  • c: cross-talk score

  • S1_size,S2_size: number of genes in S1 and S2

  • S1_s2_size,S2_s1_size: number of S1 genes interacting with S2, and vice versa

  • dL: number of links between S1 and S2

  • L: number of possible links between S1 and S2

  • r_c: cross-talk saturation, calculated as `dL/L`

  • u1,u2: sum of the gene weights in S1 and S2, respectively

  • S1,S2: list of interacting genes in S1 and S2, respectively

  • s: cross-talk summary score

  • pA,pU: p-values of the number of links (pA) and weights (pU)

  • p: combined p-value

Details

The function takes as inputs takes as input the list of communication details of interest (`ccc_list`), together with the cluster-list used for CCC calculation (`cl_list`), a list of gene sets lists (`gs_list`), one for each cluster/cell type, and the adjacency matrix of the biological network (`A`). These inputs are formatted and passed to `single_integrated_cross_talk()` to calculate integrated cross-talk on each cluster pair provided.