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Run SecAct secreted protein activity inference

Source: R/RunSecAct.R
RunSecAct.Rd

Run the optional SecAct R package from scop to infer secreted protein signaling activity from bulk, single-cell, or spatial transcriptomics profiles. SecAct is not bundled with scop; it is checked and installed from data2intelligence/SecAct when this function is called.

Usage

RunSecAct(
  srt = NULL,
  inputProfile = NULL,
  inputProfile_control = NULL,
  mode = c("auto", "matrix", "scRNAseq", "ST"),
  assay = NULL,
  layer = "counts",
  cellType_meta = NULL,
  is.singleCellLevel = FALSE,
  is.differential = FALSE,
  is.paired = FALSE,
  is.singleSampleLevel = FALSE,
  scale.factor = NULL,
  sigMatrix = "SecAct",
  is.filter.sig = FALSE,
  is.group.sig = TRUE,
  is.group.cor = 0.9,
  lambda = 5e+05,
  nrand = 1000,
  ncores = 1L,
  backend = "auto",
  rng_method = "mt19937",
  batch_size = NULL,
  output_h5 = NULL,
  activity = c("zscore", "beta", "se", "pvalue"),
  assay_out = "SecAct",
  store_assay = !is.null(srt),
  store_results = TRUE,
  tool_name = "SecAct",
  return_seurat = !is.null(srt),
  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.

inputProfile_control

Optional control expression matrix or SpaCET object passed to SecAct.

mode

SecAct workflow. auto dispatches from the input class.

assay

Assay used when extracting a matrix from srt; also sets the default assay for Seurat input passed to SecAct.

layer

Assay layer used when mode = "matrix" and inputProfile is not supplied.

cellType_meta

Metadata column containing cell type or state labels for mode = "scRNAseq" when is.singleCellLevel = FALSE.

is.singleCellLevel

Whether SecAct should return single-cell activity rather than cell-state activity for Seurat input.

is.differential, is.paired, is.singleSampleLevel

Parameters passed to SecAct.activity.inference for matrix or bulk input.

scale.factor

Spot-level scale factor passed to SecAct.activity.inference.ST.

sigMatrix

SecAct signature matrix name.

is.filter.sig, is.group.sig, is.group.cor, lambda, nrand, ncores, backend, rng_method

Parameters passed to SecAct activity inference.

batch_size, output_h5

Optional large-matrix controls passed only to SecAct.activity.inference.

activity

Activity matrix to store as a Seurat assay when possible.

assay_out

Name of the Seurat assay used to store activity values.

store_assay

Whether to store a SecAct activity matrix as a Seurat assay when its columns match Seurat cells.

store_results

Whether to store raw SecAct results in srt@tools.

tool_name

Name used in srt@tools.

return_seurat

Whether to return a Seurat object when srt is supplied.

verbose

Whether to print the message. Default is TRUE.

Value

A Seurat object, SpaCET object, or SecAct result list depending on input and return_seurat.

Examples

if (FALSE) { # \dontrun{
srt <- RunSecAct(
  srt,
  mode = "scRNAseq",
  cellType_meta = "celltype",
  is.singleCellLevel = TRUE
)

res <- RunSecAct(
  inputProfile = expr_mat,
  mode = "matrix",
  is.differential = TRUE
)
} # }