R/buildReferenceLookup.R

In TJN25/comparativeSRA: Runs steps involved in the comparativeSRA analysis project

#' buildReferenceLookup Function
#'
#' @param reference The file reference positons
#' @param seqA which columns to use for the first sequence
#' @param seqB which columns to use for the second sequence
#' @param remove.missing remove rows that are not conserved
#' @param collapse.alignment combines segments which can be combines once other alignments are removed
#' @keywords Takes a full .backbone input and produces a file with two sequences, sorted and all with +ve values and strand info
#' @export
#' @examples
#' buildReferenceLookup()

buildReferenceLookup <- function(reference, seqA = 1, seqB = 2, remove.missing = T, collapse.alignment = T, quiet = F){

test_setup <- F
  if(test_setup == T){
    load("~/bin/r_git/R/buildReferenceLookupData.Rda")
    reference <- buildReferenceLookupData[["reference"]]
    gff1 <- buildReferenceLookupData[["gff1"]]
    gff2 <- buildReferenceLookupData[["gff2"]]
    seqA <- buildReferenceLookupData[["seqA"]]
    seqB <- buildReferenceLookupData[["seqB"]]
    quiet <- F
    time.it <- T
    remove_missing <- T
    i <- 0
    collapse.alignment <- buildReferenceLookupData[["collapse.alignment"]]
    test_setup <- T
  }



  refA <- reference[,(seqA*2 - 1):(seqA*2)]
  refB <- reference[,(seqB*2 - 1):(seqB*2)]
  colnames(refA) <- c("start.a", "end.a")
  colnames(refB) <- c("start.b", "end.b")


  refA <- refA%>%
    mutate(strand.a = ifelse(start.a < 0, "-", "+"))%>%
    mutate(start.a = abs(start.a))%>%
    mutate(end.a = abs(end.a))

  refB <- refB%>%
    mutate(strand.b = ifelse(start.b < 0, "-", "+"))%>%
    mutate(start.b = abs(start.b))%>%
    mutate(end.b = abs(end.b))


  ref <- refA%>%bind_cols(refB)

  if(remove.missing == T){
    ref <- ref%>%filter((start.a - end.a) != 0, (start.b - end.b) != 0)
  }
  ref <- ref%>%arrange(start.a)



  if(collapse.alignment == T){
    ref <- collapseAlignment(ref = ref)
  }

  ref <- ref%>%mutate(diff = start.a - start.b)

  return(ref)

}