✨ add further methods

- msImpute - trKNN (from source) Add to workflow check.
RasmussenLab · Sep 19, 2023 · 0517113 · 0517113
1 parent 13dba85
commit 0517113
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Showing 3 changed files with 41 additions and 28 deletions.
diff --git a/project/01_1_train_NAGuideR_methods.R b/project/01_1_train_NAGuideR_methods.R
@@ -170,12 +170,14 @@ nafunctions <- function(x,method="zero"){
     }
     else if(method=="trknn"){
       source('src/R_NAGuideR/Imput_funcs.r')
-      sim_trKNN_wrapper <- function(data) {
-        result <- data %>% as.matrix %>% t %>% imputeKNN(., k=10, distance='truncation', perc=0) %>% t
-        return(result)
-      }
-      df1x <- sim_trKNN_wrapper(t(df1))
-      df<-as.data.frame(t(df1x))
+      # sim_trKNN_wrapper <- function(data) {
+      #   result <- data %>% as.matrix %>% t %>% imputeKNN(., k=10, distance='truncation', perc=0) %>% t
+      #   return(result)
+      # }
+      # df1x <- sim_trKNN_wrapper(t(df1))
+      # df<-as.data.frame(t(df1x))
+      df <- imputeKNN(as.matrix(df), k=10, distance='truncation', perc=0)
+      df <- as.data.frame(df)
     }
     else if(method=="rf"){
       install_rpackage("missForest")
@@ -212,10 +214,15 @@ nafunctions <- function(x,method="zero"){
 
       df<-GMS.Lasso(df1,nfolds=3,log.scale=FALSE,TS.Lasso=TRUE)
     }
+    else if(method=="msimpute"){
+       install_bioconductor("msImpute")
+       df <- msImpute(as.matrix(df), method='v2')
+       df <- as.data.frame(df) 
+    }
     else{
       stop(paste("Unspported methods so far: ", method))
     }
-    df<-as.data.frame(df)
+    df <- as.data.frame(df)
     df
   }
 # -
@@ -269,8 +276,8 @@ df
 original_header <- colnames(
     readr::read_csv(train_split, n_max=1, col_names=TRUE, skip=0)
 )
-original_header
 feat_name <- original_header[1]
+original_header[1:5]
 # -
 
 # Uncomment to test certain methods (only for debugging, as at least one method per package is tested using Github Actions)
@@ -298,7 +305,9 @@ feat_name <- original_header[1]
  # 'MICE-CART',
  # 'RF',
  # 'PI',
- # 'GMS' # fails to install on Windows
+ # 'GMS', # fails to install on Windows
+ #  'trknn',
+ #  'msimpute'
 # )
 
 # for (method in to_test) {
@@ -316,7 +325,6 @@ pred <- tibble::as_tibble(
 )
 names(pred) <- original_header
 pred
-
 # + vscode={"languageId": "r"}
 pred <- reshape2::melt(pred, id.vars=feat_name)
 names(pred) <- c(feat_name, 'Sample ID', method)

diff --git a/project/01_1_train_NAGuideR_methods.ipynb b/project/01_1_train_NAGuideR_methods.ipynb
@@ -1,7 +1,6 @@
 {
  "cells": [
   {
-   "attachments": {},
    "cell_type": "markdown",
    "id": "afa6aadb-bb6e-4fa2-8c91-b69d6ff9af43",
    "metadata": {},
@@ -52,7 +51,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "id": "edec29ae-208a-403a-aa77-82782bccba87",
    "metadata": {},
@@ -61,7 +59,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "id": "c2e51b96-2f46-42c7-a642-a94c628dec04",
    "metadata": {},
@@ -198,12 +195,14 @@
     "    }\n",
     "    else if(method==\"trknn\"){\n",
     "      source('src/R_NAGuideR/Imput_funcs.r')\n",
-    "      sim_trKNN_wrapper <- function(data) {\n",
-    "        result <- data %>% as.matrix %>% t %>% imputeKNN(., k=10, distance='truncation', perc=0) %>% t\n",
-    "        return(result)\n",
-    "      }\n",
-    "      df1x <- sim_trKNN_wrapper(t(df1))\n",
-    "      df<-as.data.frame(t(df1x))\n",
+    "      # sim_trKNN_wrapper <- function(data) {\n",
+    "      #   result <- data %>% as.matrix %>% t %>% imputeKNN(., k=10, distance='truncation', perc=0) %>% t\n",
+    "      #   return(result)\n",
+    "      # }\n",
+    "      # df1x <- sim_trKNN_wrapper(t(df1))\n",
+    "      # df<-as.data.frame(t(df1x))\n",
+    "      df <- imputeKNN(as.matrix(df), k=10, distance='truncation', perc=0)\n",
+    "      df <- as.data.frame(df)\n",
     "    }\n",
     "    else if(method==\"rf\"){\n",
     "      install_rpackage(\"missForest\")\n",
@@ -240,16 +239,20 @@
     "      \n",
     "      df<-GMS.Lasso(df1,nfolds=3,log.scale=FALSE,TS.Lasso=TRUE)\n",
     "    }\n",
+    "    else if(method==\"msimpute\"){\n",
+    "       install_bioconductor(\"msImpute\")\n",
+    "       df <- msImpute(as.matrix(df), method='v2')\n",
+    "       df <- as.data.frame(df) \n",
+    "    }\n",
     "    else{\n",
     "      stop(paste(\"Unspported methods so far: \", method))\n",
     "    }\n",
-    "    df<-as.data.frame(df)\n",
+    "    df <- as.data.frame(df)\n",
     "    df\n",
     "  }"
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "id": "7152239b-fad2-4e0f-8b3e-98d943cab264",
    "metadata": {},
@@ -303,7 +306,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "id": "fc7ef882-0cbd-40f7-a77f-cc87f7145171",
    "metadata": {},
@@ -328,7 +330,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "id": "3ed78a0c-2716-4629-bb15-8e3fd650576a",
    "metadata": {
@@ -354,8 +355,8 @@
     "original_header <- colnames(\n",
     "    readr::read_csv(train_split, n_max=1, col_names=TRUE, skip=0)\n",
     ")\n",
-    "original_header\n",
-    "feat_name <- original_header[1]"
+    "feat_name <- original_header[1]\n",
+    "original_header[1:5]"
    ]
   },
   {
@@ -399,7 +400,9 @@
     " # 'MICE-CART',\n",
     " # 'RF',\n",
     " # 'PI',\n",
-    " # 'GMS' # fails to install on Windows\n",
+    " # 'GMS', # fails to install on Windows\n",
+    " #  'trknn',\n",
+    " #  'msimpute'\n",
     "# )\n",
     "\n",
     "# for (method in to_test) {\n",
@@ -409,7 +412,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "id": "ff4ff1c2-192e-4a48-b5b6-d80ab989b12e",
    "metadata": {},
@@ -422,6 +424,7 @@
    "execution_count": null,
    "id": "690d47c2-5666-41f2-b13f-9215334f197c",
    "metadata": {
+    "lines_to_next_cell": 0,
     "tags": [],
     "vscode": {
      "languageId": "r"
@@ -514,7 +517,7 @@
    "mimetype": "text/x-r-source",
    "name": "R",
    "pygments_lexer": "r",
-   "version": "3.6.3"
+   "version": "4.1.3"
   }
  },
  "nbformat": 4,

diff --git a/project/config/single_dev_dataset/example/config.yaml b/project/config/single_dev_dataset/example/config.yaml
@@ -21,3 +21,5 @@ NAGuideR_methods:
   - MICE-NORM # mice
   - MLE # norm
   - IRM # VIM - ~9mins
+  - TRKNN
+  - MSIMPUTE