Importing_Data.Rmd

---
title: "Reading 12 Fingerprint from Padel Descriptor Calculator"
author: Saw Simeon, Nuttapat Anuwongcharoen, Watshara Shoombuatong, Aijaz Ahmad Malik,
  Virapong Prachayasittikul, Jarl E. S. Wikberg and Chanin Nantasenamat
date: "June 8, 2016"
output: pdf_document
---

### Function for Correlation Cut of at 0.7

```{r}
### Regression Acetylachlineesterase
read_file <- function(x){
  library(caret)
  library(data.table)
  data <- fread(x)
  IC50_nm <- data$IC50
  IC50 <- as.numeric(IC50_nm)*10^-9
  pIC50 <- -log10(IC50)
  data <- as.data.frame(data)
  descriptors <- data[, 2:ncol(data)]
  set.seed(1)
  yes <- descriptors[, -nearZeroVar(descriptors)]
  raw <- cor(yes)
  raw_2 <- raw[1: ncol(raw), 1:ncol(raw)]
  high <- findCorrelation(raw_2, cutoff = 0.7)
  filtered_descriptors <- yes[, -high]
  filtered_data <- cbind(pIC50, filtered_descriptors)
  return(filtered_data)
}

```

### Reading each data frame and printing out of the dimension of each data Frame 

```{r, eval = TRUE}

AtomPairs2D_fingerPrintCount <- read_file("data/2D_Atom_Paris_Count.csv")
AtomPairs2D_fingerPrinter <- read_file("data/2D_Atom_Pairs.csv")
Substructure_fingerPrintCount <- read_file("data/Substructure_Count.csv")
Substructure_fingerPrinter <- read_file("data/Substructure.csv")
Extended_finterPrinter <- read_file("data/CDK_Extended.csv")
FingerPrinter <- read_file("data/CDK.csv")
Estate_FingerPrinter <- read_file("data/E_State.csv")
GraphOnly_FingerPrinter <- read_file("data/CDK_Graph_Only.csv")
KlekotaRoth_FingerprintCount <- read_file("data/Klekota_Roth_Count.csv")
KlekotaRoth_FingerPrinter <- read_file("data/Klekota_Roth.csv")
MACCS_FingerPrinter <- read_file("data/MACCS.csv")
Pubchem_FingerPrinter <- read_file("data/PubChem.csv")


input <- list(AtomPairs2D_fingerPrintCount=AtomPairs2D_fingerPrintCount,
              AtomPairs2D_fingerPrinter = AtomPairs2D_fingerPrinter,
              Substructure_fingerPrintCount = Substructure_fingerPrintCount,
              Substructure_fingerPrinter = Substructure_fingerPrinter,
              Extended_finterPrinter = Extended_finterPrinter,
              FingerPrinter = FingerPrinter,
              Estate_FingerPrinter = Estate_FingerPrinter,
              GraphOnly_FingerPrinter = GraphOnly_FingerPrinter,
              KlekotaRoth_FingerprintCount = KlekotaRoth_FingerprintCount,
              KlekotaRoth_FingerPrinter = KlekotaRoth_FingerPrinter,
              MACCS_FingerPrinter = MACCS_FingerPrinter,
              Pubchem_FingerPrinter = Pubchem_FingerPrinter)

print(lapply(input, function(x) dim(x)))

```