Infer the signaling activity of 1248 secreted proteins from gene expression profiles.
Usage
SecAct.activity.inference(
inputProfile,
inputProfile_control = NULL,
is.differential = FALSE,
is.paired = FALSE,
is.singleSampleLevel = FALSE,
sigMatrix = "SecAct",
is.group.sig = TRUE,
lambda = 5e+05,
nrand = 1000,
sigFilter = FALSE
)Arguments
- inputProfile
Gene expression matrix with gene symbol (row) x sample (column).
- inputProfile_control
Gene expression matrix with gene symbol (row) x sample (column).
- is.differential
A logical indicating whether inputProfile has been differential profiles against to control.
- is.paired
A logical indicating whether you want a paired operation of differential profiles between inputProfile and inputProfile_control if samples in inputProfile and inputProfile_control are paired.
- is.singleSampleLevel
A logical indicating whether to calculate activity change for each single sample between inputProfile and inputProfile_control. If FALSE, calculate the overall activity change between two phenotypes.
- 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.