version 1.1.0 released. Includes functions for MAR/MNAR diagnosis, and quantification of distortion to global and local structures post imputation.

Author: soroorh

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: msImpute
 Type: Package
 Title: Peptide imputation in label-free proteomics
-Version: 0.1.0
+Version: 1.1.0
 Authors@R: 
     person(given = "Soroor",
            family = "Hediyeh-zadeh",

R/msImpute.R

@@ -59,7 +59,11 @@ msImpute <- function(object, rank.max = NULL, lambda = NULL, thresh = 1e-05,
                   maxit = maxit, trace.it = trace.it, warm.start = warm.start, final.svd = final.svd)
   cat("model fitted. \nImputting missing entries ... \n")
   ximp <- softImpute::complete(x, fit)
-  cat("Imputation completed \n")  # need to print out final rank model fitted
+  cat("Imputation completed \n")  # need to define a print method for final rank model fitted
+
+  if(any(object < 0)){
+    warning("Negative values encountered in imputed data. Please consider revising filtering and/or normalisation steps.")
+  }
 
   if(is(object,"MAList")) {
     object$E <- ximp