Import a bam file into R

readBAM.R

# install the Rsamtools package if necessary
source("http://bioconductor.org/biocLite.R")
biocLite("Rsamtools")
 
# load the library
library(Rsamtools)

# specify the bam file you want to import
bamFile <- "test.bam"

# A function to read bam file

readBAM <- function(bamFile){

  bam <- scanBam(bamFile)
  
  # A function for collapsing the list of lists into a single list
  # as per the Rsamtools vignette
  .unlist <- function (x){
    x1 <- x[[1L]]
    if (is.factor(x1)){
      structure(unlist(x), class = "factor", levels = levels(x1))
    } else {
      do.call(c, x)
    }
  }
  
  bam_field <- names(bam[[1]])
  
  list <- lapply(bam_field, function(y) .unlist(lapply(bam, "[[", y)))
  
  bam_df <- do.call("DataFrame", list)
  names(bam_df) <- bam_field

  #return a list that can be called as a data frame
  return(bam_df)
}

# Load the bam file
bam1 <- readBAM(bamFile)

Hi Sam,

I am trying to read a BAM file and it takes a long time and it fails.

Do you have any recommendation?

Best,