Run SecAct cell-cell communication analysis

Run SecAct cell-cell communication modules for Seurat scRNA-seq input or SpaCET single-cell-resolution spatial transcriptomics input.

Usage

RunSecActCCC(
  srt = NULL,
  inputProfile = NULL,
  mode = c("scRNAseq", "scST"),
  cellType_meta,
  condition_meta = NULL,
  conditionCase = NULL,
  conditionControl = NULL,
  scale.factor = NULL,
  act_diff_cutoff = 2,
  exp_logFC_cutoff = 0.2,
  exp_mean_all_cutoff = 2,
  exp_fraction_case_cutoff = 0.1,
  padj_cutoff = 0.01,
  sigMatrix = "SecAct",
  is.group.sig = TRUE,
  is.group.cor = 0.9,
  lambda = 5e+05,
  nrand = 1000,
  radius = 20,
  ratio_cutoff = 0.2,
  coreNo = 6,
  tool_name = "SecAct_CCC",
  store_results = TRUE,
  verbose = TRUE
)

Arguments

srt: Optional Seurat object. When mode = "scRNAseq", this is passed to SecAct.activity.inference.scRNAseq. When mode = "matrix", expression is extracted from srt if inputProfile is not supplied.
inputProfile: Expression matrix, Seurat object, or SpaCET object. Matrix input must be genes x samples, cells, or spatial spots.
mode: scRNAseq or scST.
cellType_meta: Metadata column containing cell type or state labels for mode = "scRNAseq" when is.singleCellLevel = FALSE.
condition_meta: Metadata column containing condition labels for scRNA-seq CCC.
conditionCase, conditionControl: Case and control labels for scRNA-seq CCC.
scale.factor: Spot-level scale factor passed to SecAct.activity.inference.ST.
act_diff_cutoff, exp_logFC_cutoff, exp_mean_all_cutoff, exp_fraction_case_cutoff, padj_cutoff: Cutoffs passed to SecAct.CCC.scRNAseq.
sigMatrix: SecAct signature matrix name.
is.group.sig, is.group.cor, lambda, nrand: Parameters passed to SecAct signature grouping and randomization routines.
radius, ratio_cutoff, coreNo: Parameters passed to SecAct.CCC.scST.
tool_name: Name used in srt@tools.
store_results: Whether to store raw SecAct results in srt@tools.
verbose: Whether to print the message. Default is TRUE.

Value

A Seurat or SpaCET object with SecAct CCC results.