Calculate secreted protein signaling activity of spots from spatial transcriptomocs data.
Usage
SecAct.activity.inference.ST(
inputProfile,
inputProfile_control = NULL,
scale.factor = 1e+05,
sigMatrix = "SecAct",
is.group.sig = TRUE,
lambda = 5e+05,
nrand = 1000,
sigFilter = FALSE
)Arguments
- inputProfile
A SpaCET object.
- inputProfile_control
A SpaCET object.
- scale.factor
Sets the scale factor for spot-level normalization.
- sigMatrix
Secreted protein signature matrix.
- is.group.sig
A logical indicating whether to group similar signatures.
- lambda
Penalty factor in the ridge regression.
- nrand
Number of randomization in the permutation test, with a default value 1000.
- sigFilter
A logical indicating whether filter the secreted protein signatures with the genes from inputProfile.