Loader for mutationTimeR (get_timed_mutations)

.Rbuildignore

@@ -1,3 +1,4 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^LICENSE\.md$
+^vignettes/articles$

NAMESPACE

@@ -59,6 +59,7 @@ export(get_ssh_session)
 export(get_ssm_by_regions)
 export(get_ssm_by_samples)
 export(get_study_info)
+export(get_timed_mutations)
 export(id_ease)
 export(link_seq_types)
 export(maf_to_custom_track)

R/annotate_maf_triplet.R

@@ -32,48 +32,47 @@
 #' @export
 #'
 #' @examples
-#' maf <- GAMBLR.open::get_coding_ssm(projection="hg38") %>% head(n=500)
+#' maf <- GAMBLR.open::get_coding_ssm(projection = "hg38") %>% head(n = 500)
 #' # peek at the data
-#' dplyr::select(maf,1:12) %>% head()
+#' dplyr::select(maf, 1:12) %>% head()
 #'
 #' maf_anno <- annotate_maf_triplet(maf)
-#' dplyr::select(maf_anno,1:12,seq) %>% head()
+#' dplyr::select(maf_anno, 1:12, seq) %>% head()
 #' # Each mutation is now associated with it's sequence context in the
 #' # reference genome in a column named seq
 #' \dontrun{
-#'   annotate_maf_triplet(maf, all_SNVs = FALSE, "C", "T")
-#'   annotate_maf_triplet(maf, ref = "C", alt = "T", pyrimidine_collapse = TRUE)
+#' annotate_maf_triplet(maf, all_SNVs = FALSE, "C", "T")
+#' annotate_maf_triplet(maf, ref = "C", alt = "T", pyrimidine_collapse = TRUE)
 #' }
-
-annotate_maf_triplet = function(maf,
-                                all_SNVs = TRUE,
-                                ref,
-                                alt,
-                                genome_build,
-                                fastaPath,
-                                pyrimidine_collapse = FALSE){
-  genome = ""
+annotate_maf_triplet <- function(maf,
+                                 all_SNVs = TRUE,
+                                 ref,
+                                 alt,
+                                 genome_build,
+                                 fastaPath,
+                                 pyrimidine_collapse = FALSE) {
+  genome <- ""
   # Get projection from NCBI_Build column of the maf
   if ("NCBI_Build" %in% colnames(maf)) {
-    genome_build = tolower(maf$NCBI_Build[1])
+    genome_build <- tolower(maf$NCBI_Build[1])
   } # If it is not in the maf, look for it in bsgenome_name
   else if (!missing(bsgenome_name)) {
-    bsgenome_parts = unlist(strsplit(bsgenome_name, "\\."))
-    genome_build = bsgenome_parts[4]
+    bsgenome_parts <- unlist(strsplit(bsgenome_name, "\\."))
+    genome_build <- bsgenome_parts[4]
   } # Cannot find it ask for mutating it
-  else{
+  else {
     stop("Please add the 'NCBI_Build' column to your MAF file to specify the genome build.")
   }
-  bsgenome_loaded = FALSE
+  bsgenome_loaded <- FALSE
 
   # If there is no fastaPath, it will read it from config key
 
   # Based on the genome_build the fasta file which will be loaded is different
-  if (missing(fastaPath)){
-    if("maf_data" %in% class(maf)){
-      genome_build = get_genome_build(maf)
+  if (missing(fastaPath)) {
+    if ("maf_data" %in% class(maf)) {
+      genome_build <- get_genome_build(maf)
     }
-    if(missing(genome_build)){
+    if (missing(genome_build)) {
       stop("no genome_build information provided or present in maf")
     }
     base <- check_config_value(config::get("repo_base"))
@@ -83,145 +82,144 @@ annotate_maf_triplet = function(maf,
       genome_build,
       "/genome_fasta/genome.fa"
     )
-    if(!file.exists(fastaPath)){
-      #try BSgenome
-      installed = installed.genomes()
-      if(genome_build=="hg38"){
-        bsgenome_name = "BSgenome.Hsapiens.UCSC.hg38"
-      }else if(genome_build == "grch37"){
-        bsgenome_name = "BSgenome.Hsapiens.NCBI.GRCh37"
-      }else{
-        stop(paste("unsupported genome:",genome_build))
+    if (!file.exists(fastaPath)) {
+      # try BSgenome
+      installed <- installed.genomes()
+      if (genome_build == "hg38") {
+        bsgenome_name <- "BSgenome.Hsapiens.UCSC.hg38"
+      } else if (genome_build == "grch37") {
+        bsgenome_name <- "BSgenome.Hsapiens.NCBI.GRCh37"
+      } else {
+        stop(paste("unsupported genome:", genome_build))
       }
-      if(bsgenome_name %in% installed){
-          genome = getBSgenome(bsgenome_name)
-          bsgenome_loaded = TRUE
-      }else{
+      if (bsgenome_name %in% installed) {
+        genome <- getBSgenome(bsgenome_name)
+        bsgenome_loaded <- TRUE
+      } else {
         print(installed)
-        print(paste("Local Fasta file cannot be found and missing genome_build",bsgenome_name,"Supply a fastaPath for a local fasta file or install the missing BSGenome package and re-run"))
+        print(paste("Local Fasta file cannot be found and missing genome_build", bsgenome_name, "Supply a fastaPath for a local fasta file or install the missing BSGenome package and re-run"))
       }
     }
   }
   # It checks for the presence of a local fastaPath
-  if(!bsgenome_loaded){
+  if (!bsgenome_loaded) {
     # Create a reference to an indexed fasta file.
     if (!file.exists(fastaPath)) {
       stop("Failed to find the fasta file and no compatible BSgenome found")
     }
-    fasta = Rsamtools::FaFile(file = fastaPath)
+    fasta <- Rsamtools::FaFile(file = fastaPath)
   }
 
   # Store the complement of ref and alt alleles
   complement <- c(
-    'A'= 'T',
-    'T'= 'A',
-    'C'= 'G',
-    'G'= 'C'
+    "A" = "T",
+    "T" = "A",
+    "C" = "G",
+    "G" = "C"
   )
-  if(pyrimidine_collapse){
+  if (pyrimidine_collapse) {
     maf <- maf %>%
-        dplyr::mutate(
-            mutation_strand=ifelse(
-                Reference_Allele %in% c("A","G"),
-                    "-",
-                        "+"
-            )
-        ) %>%
-        dplyr::mutate(
-            mutation = ifelse(
-                Reference_Allele %in% c("A","G"),
-                     paste0(complement[Reference_Allele],">",complement[Tumor_Seq_Allele2]),
-                        paste0(Reference_Allele,">",Tumor_Seq_Allele2)))
-  }else{
-    maf = dplyr::mutate(
-        maf,
-        mutation_strand="+")
+      dplyr::mutate(
+        mutation_strand = ifelse(
+          Reference_Allele %in% c("A", "G"),
+          "-",
+          "+"
+        )
+      ) %>%
+      dplyr::mutate(
+        mutation = ifelse(
+          Reference_Allele %in% c("A", "G"),
+          paste0(complement[Reference_Allele], ">", complement[Tumor_Seq_Allele2]),
+          paste0(Reference_Allele, ">", Tumor_Seq_Allele2)
+        )
+      )
+  } else {
+    maf <- dplyr::mutate(
+      maf,
+      mutation_strand = "+"
+    )
   }
 
-  CompRef = complement[ref]
-  CompAlt = complement[alt]
+  CompRef <- complement[ref]
+  CompAlt <- complement[alt]
   # Provide triple sequence for all the SNVs
-    # Using BSgenome
-  if (all_SNVs == TRUE){
-    if(bsgenome_loaded){
+  # Using BSgenome
+  if (all_SNVs == TRUE) {
+    if (bsgenome_loaded) {
       sequences <- maf %>%
         dplyr::mutate(
           seq = ifelse(
             (nchar(maf$Reference_Allele) == 1 &
-               nchar(maf$Tumor_Seq_Allele2) == 1
+              nchar(maf$Tumor_Seq_Allele2) == 1
             ),
             as.character(
-                Rsamtools::getSeq(
-                    genome,
-                    maf$Chromosome,
-                    start = maf$Start_Position-1,
-                    end = maf$Start_Position + 1,
-                    strand = mutation_strand
-                )
+              Rsamtools::getSeq(
+                genome,
+                maf$Chromosome,
+                start = maf$Start_Position - 1,
+                end = maf$Start_Position + 1,
+                strand = mutation_strand
+              )
             ),
             "NA"
           )
         )
-
-    }else{
+    } else {
       # Using local Fasta file
       sequences <- maf %>%
         dplyr::mutate(
           seq = ifelse(
             (nchar(maf$Reference_Allele) == 1 &
-               nchar(maf$Tumor_Seq_Allele2) == 1
+              nchar(maf$Tumor_Seq_Allele2) == 1
             ),
             as.character(
-                Rsamtools::getSeq(
-                    fasta,
-                    GenomicRanges::GRanges(
-                        maf$Chromosome,
-                        IRanges(
-                            start = maf$Start_Position - 1,
-                            end = maf$Start_Position + 1
-                        ),
-                            strand = maf$mutation_strand
-                    )
+              Rsamtools::getSeq(
+                fasta,
+                GenomicRanges::GRanges(
+                  maf$Chromosome,
+                  IRanges(
+                    start = maf$Start_Position - 1,
+                    end = maf$Start_Position + 1
+                  ),
+                  strand = maf$mutation_strand
                 )
+              )
             ),
             "NA"
           )
         )
-
     }
-
-  }else{
+  } else {
     # Provide triple sequence of + strand and reverse complement of - strand
     # Mutations on + strand with chosen ref and alt alleles
     # Mutations on - strand with complement ref and alt alleles
     sequences <- maf %>%
       dplyr::mutate(
         seq = ifelse(
           (maf$mutation_strand == "+" &
-             maf$Reference_Allele == ref &
-             maf$Tumor_Seq_Allele2 == alt
-          )|(
+            maf$Reference_Allele == ref &
+            maf$Tumor_Seq_Allele2 == alt
+          ) | (
             maf$mutation_strand == "-" &
               maf$Reference_Allele == CompRef &
               maf$Tumor_Seq_Allele2 == CompAlt
           ),
           as.character(
-              Rsamtools::getSeq(
-                 fasta,
-                 GenomicRanges::GRanges(
-                    maf$Chromosome,
-                    IRanges(
-                        start = maf$Start_Position - 1,
-                        end = maf$Start_Position + 1
-                    ),
-                        strand = maf$mutation_strand
-                 )
-             )
+            Rsamtools::getSeq(
+              fasta,
+              GenomicRanges::GRanges(
+                maf$Chromosome,
+                IRanges(
+                  start = maf$Start_Position - 1,
+                  end = maf$Start_Position + 1
+                ),
+                strand = maf$mutation_strand
+              )
+            )
           ),
           "NA"
         )
       )
-
   }
   return(sequences)
 }