Update grpregOverlap.R

[LamineTourelab]

Hi Yaohui,
Thank you for your interesting package.
While working with it, I had an error with the ExpandX function with the dimnames in the Overlap matrix.
I propose this:

expandX <- function(X, group) {
  incidence.mat <- incidenceMatrix(X, group) # group membership incidence matrix
  over.mat <- Matrix(incidence.mat %*% t(incidence.mat), sparse = TRUE) 
                    # dimnames = dimnames(incidence.mat)) # overlap matrix
  grp.vec <- rep(1:nrow(over.mat), times = diag(over.mat)) # group index vector
  
  # expand X to X.latent
  X.latent <- NULL
  names <- NULL

  ## the following code will automatically remove variables not included in 'group'
  for(i in 1:nrow(incidence.mat)) {
    idx <- incidence.mat[i,]==1
    X.latent <- cbind(X.latent, X[, idx, drop=FALSE])
    names <- c(names, colnames(incidence.mat)[idx])
#     colnames(X.latent) <- c(colnames(X.latent), colnames(X)[incidence.mat[i,]==1])
  }
  colnames(X.latent) <- paste('grp', grp.vec, '_', names, sep = "")
  X.latent
}

Because when creating the overlap matrix, the dimnames are not the same with the incidence matrix.
Thanks you,
Best