R/imputation-methods.R

In dcellwanger/CellTrails: Reconstruction, visualization and analysis of branching trajectories

# #' DEF: Imputation of drop-outs
# #'
# #' For details see \code{imputeDropouts}
# #' @importFrom igraph neighbors
# #' @import Biobase
# #' @keywords internal
# #' @author Daniel C. Ellwanger
# .imputeDropouts_def <- function(x, feature_name) {
#   X <- x[feature_name, x@useSample]
#   X[X == 0] <- NA
#   g <- x@trajectory$traj
#   rep.total <- sum(is.na(X))
#
#   f.impute <- function(g, y) {
#     nds <- which(is.na(y))
#     for(nd in nds) {
#       nghbr <- as.vector(neighbors(g, V(g)[nd]))
#       y[nd] <- mean(y[nghbr])
#     }
#     y[is.na(y)] <- 0
#     y
#   }
#
#   message("Performing imputation for ", length(feature_name), " features...")
#   X.imp <- X
#   rep.f <- round(nrow(X) * .1)
#   for(i in seq_len(nrow(X))) {
#     X.imp[i, ] <- f.impute(g = g, y = X[i, ])
#     if(i %% rep.f == 0) {
#       rep.ana <- (rep.total - sum(is.na(X.imp)))
#       rep.douts <- round((rep.ana-sum(X.imp==0, na.rm=TRUE))/rep.ana*100,
#                          1)
#       message(round(rep.ana / rep.total * 100), "% non-detects analyzed (",
#               rep.douts, "% drop-outs) ...")
#     }
#   }
#   message("100% non-detects analyzed (",
#           round(sum(X.imp[is.na(X)] != 0) / rep.total * 100, 1),
#           "% drop-outs).")
#   X.imp[is.na(X.imp)] <- 0
#   exprs(x)[feature_name, x@useSample] <- X.imp
#   x
# }