Infer the activity of over 1000 secreted proteins from tumor gene expression profiles.
Usage
SecAct.inference(Y, SigMat = "SecAct", lambda = 5e+05, nrand = 1000)
Arguments
- Y
Gene expression matrix with gene symbol (row) x sample (column).
- SigMat
Secreted protein signature matrix.
- lambda
Penalty factor in the ridge regression.
- nrand
Number of randomizations in the permutation test, with a default value 1000.
Value
A list with four items, each is a matrix.
beta: regression coefficients
se: standard errors of coefficients
zscore: beta/se
pvalue: statistical significance