Preprocessing.Rmd

---
title: "Preprocessing"
output: html_document
---

GOALS:

+ Read encoded data
+ Preliminary feature selection:
  + Filter constant features
  + Filter correlated features

Setup workspace

```{r setup, include=FALSE}
getwd()
library(janitor)
library(caret)
```

Preprocessing function
  - remove constant features
  - remove highly correlated features (> 0.8)

```{r preprocess_function}
preprocessData <- function(path) {
  print("reading file...")
  data <- read.csv(path)
  print("removing constant features...")
  data <- remove_constant(data)
  # print("calculation correlations...")
  # corr <- cor(data, method = "spearman")
  # featuresToRemove <- findCorrelation(corr, cutoff = 0.8)
  # if (featuresToRemove != 0) {
  #   print(paste(
  #     "removing",
  #     length(featuresToRemove),
  #     "correlated features..."
  #   ))
  #   data <- subset(data, select = -featuresToRemove)
  # }
  print(paste("cleaned dataset contains", ncol(data), "features."))
  return(data)
}
```

Read & preprocess ace vaxinpad

```{r message=FALSE, warning=FALSE}
ace_vaxinpad <-
  preprocessData("../Data/ace_vaxinpad/ace_vaxinpad_binary_centered.csv")
ace_vaxinpad_classes <-
  read.csv("../Data/ace_vaxinpad/ace_vaxinpad_classes.txt", header = F)
ace_vaxinpad_classes <-
  factor(ace_vaxinpad_classes[, 1], labels = c("No", "Yes"))
```

Read & preprocess HIV protease

```{r message=FALSE, warning=FALSE}
hiv_protease <-
  preprocessData("../Data/hiv_protease/hiv_protease_binary_centered.csv")
hiv_protease_classes <-
  read.csv("../Data/hiv_protease/hiv_protease_classes.txt", header = F)
hiv_protease_classes <-
  factor(hiv_protease_classes[, 1], labels = c("No, Yes"))
```

Train / Test split

```{r}
set.seed(69)
trainIndACE <- createDataPartition(y = ace_vaxinpad_classes, p = 0.8, list = F)
trainIndHIV <- createDataPartition(y = hiv_protease_classes, p = 0.8, list = F)
```

Classes

```{r}
ace_vaxinpad_classes_train <- ace_vaxinpad_classes[trainIndACE]
ace_vaxinpad_classes_test <- ace_vaxinpad_classes[-trainIndACE]

hiv_protease_classes_train <- ace_vaxinpad_classes[trainIndHIV]
hiv_protease_classes_test <- ace_vaxinpad_classes[-trainIndHIV]
```

Original data sets

```{r}
ace_vaxinpad_train <- ace_vaxinpad[trainIndACE, ]
ace_vaxinpad_test <- ace_vaxinpad[-trainIndACE, ]

hiv_protease_classes_train <- hiv_protease[trainIndHIV, ]
hiv_protease_classes_test <- hiv_protease[-trainIndHIV, ]
```