Fix warnings introduced by recent PRs

R/StructuralVariants.R

@@ -20,6 +20,9 @@
 #' @aliases exampleDoubleInversion1 exampleDoubleInversion2
 #' @aliases exampleDoubleInversion3 exampleDoubleInversion4
 #' @aliases exampleTwinInversions exampleNotTwinInversions
+#' @aliases exampleInversionGarg2019 exampleInversionBader2001 
+#' @aliases exampleInversionHP1999fig4a exampleInversionHP1999fig4b 
+#' @aliases exampleInversionBergeron2005a exampleInversionBergeron2005b
 #' @aliases exampleTranslocation exampleTranslocation2
 #' @aliases exampleInsertion exampleDeletion
 #'
@@ -35,6 +38,12 @@
 #' exampleNestedInversions
 #' exampleDoubleInversion1
 #' exampleTwinInversions
+#' exampleInversionGarg2019
+#' exampleInversionBader2001
+#' exampleInversionHP1999fig4a
+#' exampleInversionHP1999fig4b
+#' exampleInversionBergeron2005a
+#' exampleInversionBergeron2005b
 #' exampleTranslocation
 #' exampleTranslocation2
 #'

R/breakpointGraph.R

@@ -78,6 +78,14 @@ breakpoint_graph <- function(p_extended) {
 
 #' Interleaving Check
 #'
+#' This function checks if two edges are interleaving.
+#'
+#' @param p_extended The extended permutation.
+#' @param graph_1 A cycle in the breakpoint graph.
+#' @param graph_2 A cycle in the breakpoint graph.
+#' @param edge_1 An edge in the breakpoint graph.
+#' @param edge_2 An edge in the breakpoint graph.
+#'
 #' @importFrom igraph E V E<- V<- ends
 #'
 #' @author Bruna Fistarol
@@ -118,7 +126,7 @@ bp_count <- function(p_extended){
 #'
 #' This function computes the number of cycles in a breakpoint graph.
 #'
-#' @param p_extended The extended permutation.
+#' @param g The breakpoint graph.
 #'
 #' @return The number of cycles in a breakpoint graph.
 #'
@@ -202,7 +210,10 @@ components_graph <- function(g, p_extended) {
 
 #' Count hurdles
 #'
-#' Count hurdles in the breakpoint graph.
+#' This function finds hurdles in the breakpoint graph and returns them.
+#'
+#' @param g The breakpoint graph.
+#' @param query_sequence_unsig The extended permutation.
 #'
 #' @importFrom igraph E V E<- V<- components ends
 #'
@@ -325,7 +336,11 @@ hurdles_count <- function(g, query_sequence_unsig){
 
 #' Count superhurdles
 #' 
-#' Counts superhurdles in the breakpoint graph.
+#' This function finds superhurdles in the breakpoint graph by checking which hurdles are superhurdles.
+#'
+#' @param info Object that stores the hurdles in the breakpoint graph.
+#' @param g The breakpoint graph.
+#' @param query_sequence_unsig The extended permutation.
 #'
 #' @importFrom igraph E V E<- V<- components ends
 #'
@@ -492,6 +507,9 @@ superhurdles_count <- function(info, g, query_sequence_unsig){
 #' Check fortrees
 #' 
 #' Check whether or not the permutation is a fortress.
+#' A permutation is a fortress if the number of hurdles is odd and all hurdles are superhurdles.
+#'
+#' @param superhurdles Object that stores the counts of hurdles and superhurdles in the breakpoint graph.
 #'
 #' @author Bruna Fistarol
 #'

R/inversionDistance.R

@@ -27,7 +27,8 @@
 #' inversionDistance(c(1, 3, -2, 4))
 #'
 #' # Example using a GBreaks object.
-#' # This example is based on Figure 4(a) from Hannehalli and Pevzner (1999). The inversion distance is 8.
+#' # This example is based on Figure 4(a) from Hannehalli and Pevzner (1999). 
+#' # The inversion distance is 8.
 #' inversionDistance(exampleInversionHP1999fig4a)
 #'
 #' @seealso \code{\link{permutationVector}} for generating the permutation vector.

R/inversionEstimate_BD.R

@@ -280,22 +280,27 @@ inversionEstimate_BD_many <- function(n, obs_nb_cycles, cyc_all=NA){
 #'
 #' @examples
 #' \dontrun{
-#' 
 #' # Create a chromosome mapping given a GBreaks object (useful when genomes are multichromosomal).
 #' chrMapping <- matchPairs(exampleInversionBader2001)
 #' # Compute the expected number of inversions using the method from Berestycki and Durrett (2006).
 #' expNbInversions <- inversionEstimate_BD(chrMapping)
 #' # Compute the minimum number of inversions using the method from Hannehalli and Pevzner (1999).
 #' minNbInversions <- inversionDistance(chrMapping)
-#' # Output: Example from Bader et al. (2001): Inversion distance = 7 , Expected nb. of inversions = 7
-#' cat(paste("Example from Bader et al. (2001): Inversion distance =", minNbInversions, ", Expected nb. of inversions =", expNbInversions[[1]]$expinv_BD$k_avg))
+#' # Output: Example from Bader et al. (2001): 
+#' #         - Inversion distance = 7 , Expected nb. of inversions = 7
+#' cat("Example from Bader et al. (2001):")
+#' cat(paste("- Inversion distance =", minNbInversions))
+#' cat(paste("- Expected nb. of inversions =", expNbInversions[[1]]$expinv_BD$k_avg))
 #' 
 #' # Another example, this time without computing the chromosome mapping.
 #' # The chromosome mapping is not needed if genomes are unichromosomal.
 #' expNbInversions <- inversionEstimate_BD(exampleInversionBergeron2005b)
 #' minNbInversions <- inversionDistance(exampleInversionBergeron2005b)
-#' # Output: Example used in the book ``Mathematics of Evolution and Phylogeny`` (2005) (Figure 10.6): Inversion distance = 13 , Expected nb. of inversions = 15
-#' cat(paste("Example used in the book ``Mathematics of Evolution and Phylogeny`` (2005) (Figure 10.6): Inversion distance =", minNbInversions, ", Expected nb. of inversions =", expNbInversions[[1]]$expinv_BD$k_avg))
+#' # Output: Example used in the book ``Mathematics of Evolution and Phylogeny`` (2005) (Figure 10.6): 
+#' #         - Inversion distance = 13 , Expected nb. of inversions = 15
+#' cat("Example used in the book ``Mathematics of Evolution and Phylogeny`` (2005) (Figure 10.6):")
+#' cat(paste("- Inversion distance =", minNbInversions))
+#' cat(paste("- Expected nb. of inversions =", expNbInversions[[1]]$expinv_BD$k_avg))
 #' }
 #'
 #' @seealso \code{\link{breakpointGraphProperties}} for computing key properties of the breakpoint graph needed for this estimate.