IMPUTE2_splines.Rmd

---
title: "R Notebook"
output:
  html_notebook: default
  html_document: default
---

Genetic Map in IMPUTE2 format for all the chromosomes:
We will be extracting the positions 

```{r}

chromosome1 <- read.delim2("/home/DB2/Imputation/Splines/chr1_Beagle.map", header = F, stringsAsFactors = F)
cM <- chromosome1[,3]
physical <- chromosome1[,4]
IMPUTE2 <- matrix(0, nrow = length(physical), ncol = 3) # IMPUTE2 genetic map format
colnames(IMPUTE2) <- c("position", "COMBINED_rate.cM.Mb.", "Genetic_Map.cM.")
IMPUTE2[,1] <- as.numeric(physical)
IMPUTE2[,3] <- as.numeric(cM)


```

Now we will calculate the Recombination rate for chromosome 1:

```{r}

for (i in 1:(dim(IMPUTE2)[1]-1)){
  # CM between markers
  cm <- as.numeric(IMPUTE2[i+1,3]) - as.numeric(IMPUTE2[i,3])
  # Mb between markers
  mb <- as.numeric(IMPUTE2[i+1,1]) - as.numeric(IMPUTE2[i,1])
  # Recombination Rate
  rr <- cm/(mb/1000000)
  if (rr > 600){
    IMPUTE2[i,2] <- 0
  }else{
    IMPUTE2[i,2] <- rr
  }
}
  

```

Plotting the first chunk of the chromosome

```{r}

plot(IMPUTE2[1:25000,2])

```

Now calculate the map in IMPUTE2 format for everything

```{r}

setwd("/home/DB2/Imputation/Splines/")

for (j in 1:18) {
  chromosome <- paste("chr", j, "_Beagle.map", sep = "")
  
  chromosome1 <- read.delim2(chromosome, header = F, stringsAsFactors = F)
  cM <- chromosome1[,3]
  physical <- chromosome1[,4]
  IMPUTE2 <- matrix(0, nrow = length(physical), ncol = 3) # IMPUTE2 genetic map format
  colnames(IMPUTE2) <- c("position", "COMBINED_rate.cM.Mb.", "Genetic_Map.cM.")
  IMPUTE2[,1] <- as.numeric(physical)
  IMPUTE2[,3] <- as.numeric(cM)
    
  for (i in 1:(dim(IMPUTE2)[1]-1)){
  # CM between markers
  cm <- as.numeric(IMPUTE2[i+1,3]) - as.numeric(IMPUTE2[i,3])
  # Mb between markers
  mb <- as.numeric(IMPUTE2[i+1,1]) - as.numeric(IMPUTE2[i,1])
  # Recombination Rate
  rr <- cm/(mb/1000000)
  if (rr > 600){
    IMPUTE2[i,2] <- 0
  }else{
    IMPUTE2[i,2] <- rr
    }
  }
  
  output <- paste("chr",j,"_Impute2.map", sep = "")
  # Export the data frame in Beagle format
  write.table(IMPUTE2, file=output, sep="\t", quote = F, row.names = F, col.names = T)
}

```