R/PathMethods.R

In carltonyfakhry/geneticsCRE: geneticsCRE is an R package that performs genome-wide association study pathway analysis (GWASPA) to identify statistically significant associations between variants on gene regulatory pathways and a given phenotype

getPaths <- function(lst, path_length, Rels1, Rels2){

  # Get the paths and signedpaths
  inds <- lst$ids
  path <- c()
  signpath <- c()
  inds1 <- inds[,1]
  inds2 <- inds[,2]

  if(path_length == 1){

    Rels2_srcs <- c(Rels2$srcuid, Rels2$srcuid)
    path <- paste(Rels2_srcs[inds2], sep = "")
    signpath <- c(paste(Rels2$srcuid, " (+)", sep = ""), paste(Rels2$srcuid, " (-)", sep = ""))
    signpath <- signpath[inds2]

  }else if(path_length == 2){

    inds3 <- inds2
    inds3[inds3 > nrow(Rels2)] <- inds3[inds3 > nrow(Rels2)] - nrow(Rels2)
    srcs <- Rels2$srcuid[inds3]
    trgs <- Rels2$trguid[inds3]
    path <- paste(srcs, trgs, sep = " -> ")

    dirs1 <- ifelse(inds2 > nrow(Rels2), "(-)", "(+)")

    dirs2 <- rep("(+)", length(inds2))
    sign1 <- Rels2$sign[inds3]
    dirs2[sign1 == 1 & dirs1 == "(-)"] <- "(-)"
    dirs2[sign1 == -1 & dirs1 == "(+)"] <- "(-)"

    signpath <- paste(paste(srcs, dirs1 , sep = " "),  paste(trgs, dirs2, sep = " "), sep = " -> ")

  }else if(path_length == 3){

    srcs <- Rels1$srcuid[inds1]
    trgs <- Rels1$trguid[inds1]
    inds3 <- inds2
    inds3[inds3 > nrow(Rels2)] <- inds3[inds3 > nrow(Rels2)] - nrow(Rels2)
    trgs2 <- Rels2$trguid[inds3]
    path <- paste(srcs, trgs, trgs2, sep = " -> ")

    dirs1 <- ifelse(inds2 > nrow(Rels1), "(-)", "(+)")

    dirs2 <- rep("(+)", length(inds1))
    sign1 <- Rels1$sign[inds1]
    dirs2[sign1 == 1 & dirs1 == "(-)"] <- "(-)"
    dirs2[sign1 == -1 & dirs1 == "(+)"] <- "(-)"

    dirs3 <- rep("(+)", length(inds1))
    sign2 <- Rels2$sign[inds3]
    dirs3[sign2 == 1 & dirs2 == "(-)"] <- "(-)"
    dirs3[sign2 == -1 & dirs2 == "(+)"] <- "(-)"

    signpath <- paste(paste(srcs, dirs1 , sep = " "),  paste(trgs, dirs2, sep = " "), paste(trgs2, dirs3, sep = " "), sep = " -> ")

  }else if(path_length == 4){

    srcs <- Rels1$srcuid[inds1]
    trgs <- Rels1$trguid[inds1]
    trgs2 <- Rels1$trguid2[inds1]
    inds3 <- inds2
    inds3[inds3 > nrow(Rels2)] <- inds3[inds3 > nrow(Rels2)] - nrow(Rels2)
    trgs3 <- Rels2$trguid[inds3]
    path <- paste(srcs, trgs, trgs2, trgs3, sep = " -> ")

    dirs1 <- ifelse(inds2 > nrow(Rels2), "(-)", "(+)")

    dirs2 <- rep("(+)", length(inds1))
    sign1 <- Rels1$sign[inds1]
    dirs2[sign1 == 1 & dirs1 == "(-)"] <- "(-)"
    dirs2[sign1 == -1 & dirs1 == "(+)"] <- "(-)"

    dirs3 <- rep("(+)", length(inds1))
    sign2 <- Rels1$sign2[inds1]
    dirs3[sign2 == 1 & dirs2 == "(-)"] <- "(-)"
    dirs3[sign2 == -1 & dirs2 == "(+)"] <- "(-)"

    dirs4 <- rep("(+)", length(inds1))
    sign3 <- Rels2$sign[inds3]
    dirs4[sign3 == 1 & dirs3 == "(-)"] <- "(-)"
    dirs4[sign3 == -1 & dirs3 == "(+)"] <- "(-)"

    signpath <- paste(paste(srcs, dirs1 , sep = " "),  paste(trgs, dirs2, sep = " "), paste(trgs2, dirs3, sep = " "), paste(trgs3, dirs4, sep = " "), sep = " -> ")

  }else if(path_length == 5){

    srcs <- Rels1$srcuid[inds1]
    trgs <- Rels1$trguid[inds1]
    trgs2 <- Rels1$trguid2[inds1]
    inds3 <- inds2
    inds3[inds3 > nrow(Rels2)] <- inds3[inds3 > nrow(Rels2)] - nrow(Rels2)
    trgs3 <- Rels2$trguid[inds3]
    trgs4 <- Rels2$trguid2[inds3]
    path <- paste(srcs, trgs, trgs2, trgs3, trgs4, sep = " -> ")

    dirs1 <- ifelse(inds2 > nrow(Rels2), "(-)", "(+)")

    dirs2 <- rep("(+)", length(inds1))
    sign1 <- Rels1$sign[inds1]
    dirs2[sign1 == 1 & dirs1 == "(-)"] <- "(-)"
    dirs2[sign1 == -1 & dirs1 == "(+)"] <- "(-)"

    dirs3 <- rep("(+)", length(inds1))
    sign2 <- Rels1$sign2[inds1]
    dirs3[sign2 == 1 & dirs2 == "(-)"] <- "(-)"
    dirs3[sign2 == -1 & dirs2 == "(+)"] <- "(-)"

    dirs4 <- rep("(+)", length(inds3))
    sign3 <- Rels2$sign[inds3]
    dirs4[sign3 == 1 & dirs3 == "(-)"] <- "(-)"
    dirs4[sign3 == -1 & dirs3 == "(+)"] <- "(-)"

    dirs5 <- rep("(+)", length(inds3))
    sign4 <- Rels2$sign2[inds3]
    dirs5[sign4 == 1 & dirs4 == "(-)"] <- "(-)"
    dirs5[sign4 == -1 & dirs4 == "(+)"] <- "(-)"

    signpath <- paste(paste(srcs, dirs1 , sep = " "),  paste(trgs, dirs2, sep = " "), paste(trgs2, dirs3, sep = " "), paste(trgs3, dirs4, sep = " "), paste(trgs4, dirs5, sep = " "), sep = " -> ")

  }


  lst2 <- list()
  lst2[["path"]] <- path
  lst2[["signpath"]] <- signpath

  return(lst2)

}

getUidsCountsLocations <- function(Rels1_trgs, Rels2_srcs){

  # Handle target nodes, which are source nodes in Rels2
  unique_Rels2_srcs <- sort(unique(Rels2_srcs))
  counts_Rels2_srcs <- rle(Rels2_srcs)$lengths
  cumsum_Rels2_srcs <- cumsum(counts_Rels2_srcs)
  locations_Rels2_srcs <- cumsum_Rels2_srcs - counts_Rels2_srcs # locations of the first occurrence of the ordered source nodes in Rels2

  # Get a mapping between uid and where it occurs in Rels2 and how many times it occurs contiguously
  # (p.s it could only occur contiguously since the source column in Rels2 is assumed to be ordered)
  uids_CountLoc <- getMatchingList(unique_Rels2_srcs, counts_Rels2_srcs, locations_Rels2_srcs)

  inds <- which(!(unique(Rels1_trgs) %in% Rels2_srcs)) # account for the target nodes in Rels1 which are not present in the source nodes of Rels2
  for(i in unique(Rels1_trgs)[inds]){
    uids_CountLoc[[toString(i)]] = c(0,-1)
  }

  return(uids_CountLoc)

}