Complete documentation of subnetwork extraction and search

Author: wulingyun

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: Corbi
-Version: 0.3-4
+Version: 0.3-5
 Title: Collection of Rudimentary Bioinformatics Tools
 Description: Provides a bundle of basic and fundamental bioinformatics tools,
-    such as network querying and alignment.
+    such as network querying and alignment, subnetwork extraction and search.
 Authors@R: c(person("Ling-Yun", "Wu", role = c("aut", "cre"), email =
     "[email protected]"), person("Qiang", "Huang", role = c("aut"), email =
     "[email protected]"))

R/Corbi-package.R

@@ -1,17 +1,24 @@
-#' Corbi - Bioinformatics analysis tools
+#' Corbi - Collection of Rudimentary Bioinformatics Tools
 #' 
-#' This pakcage provides a bundle of bioinformatics analysis tools for biomedical research.
+#' This pakcage provides a bundle of basic and fundamental bioinformatics tools.
 #'
-#' This is a collection of bioinformatics analysis tools developed by WuLab at Academy of Mathematics
+#' These bioinformatics tools are developed by \href{http://wulab.aporc.org}{WuLab} at Academy of Mathematics
 #' and Systems Science, Chinese Academy of Sciences.
 #' 
-#' Network comparison:
+#' Network querying and alignment:
 #' \itemize{
 #'   \item \code{\link{net_query}} Network querying method based on conditional random fields
 #'   \item \code{\link{net_query_batch}} Batch processing version of \code{\link{net_query}}
 #'   \item \code{\link{net_align}} Network alignment method based on conditional random fields
 #' }
 #' 
+#' Subnetwork extraction and search:
+#' \itemize{
+#'   \item \code{\link{get_subnets}} Enumerate all subnetworks of limited size
+#'   \item \code{\link{extend_subnets}} Extend subnetworks from smaller subnetworks
+#'   \item \code{\link{best_subnets}} Search best subnetworks that maximize given objective function
+#' }
+#' 
 #' 
 #' @name Corbi-package
 #' @aliases Corbi-package Corbi

R/subnets.R

@@ -1,6 +1,8 @@
-#' The best subnetworks that maximize given objective function
+#' The best subnetworks
 #' 
-#' Find the best subnetworks that maximize given objective function. If the size of 
+#' Search best subnetworks that maximize given objective functions.
+#' 
+#' Enumerate and search the best subnetworks that maximize given objective function. If the size of 
 #' subnetworks <= \code{exhaust.size}, exact exhaustive searching is applied,
 #' otherwise, heuristic searching algorithm is used.
 #' 
@@ -54,7 +56,7 @@ best_subnets <- function(func, net.matrix, max.size = 10, exhaust.size = 5, max.
 }
 
 
-#' All subnetworks with limited size
+#' All subnetworks of limited size
 #' 
 #' Enumerate all subnetworks of size <= \code{max.size} from given network.
 #' 
@@ -82,12 +84,14 @@ get_subnets <- function(net.matrix, max.size = 2)
 }
 
 
-#' All subnetworks by overlapping two subnetworks
-#' 
-#' Enumerate all possible subnetworks of desired size by overlapping two sets of subnetworks
-#' of size \code{s1} and \code{s2}. The desired size should be between \code{max(s1,s2)+1} 
-#' and \code{s1+s2-1}. Invalid desired size will be replaced by the minimum allowed value 
-#' \code{max(s1,s2)+1}.
+#' Extend subnetworks from smaller subnetworks
+#'
+#' Extend subnetworks by pairwise overlapping two sets of smaller subnetworks.
+#'
+#' Enumerate all possible subnetworks of desired size by pairwise overlapping two sets of 
+#' subnetworks of size \code{s1} and \code{s2}. The desired size should be between 
+#' \code{max(s1,s2)+1} and \code{s1+s2-1}. Invalid desired size will be replaced by the 
+#' minimum allowed value \code{max(s1,s2)+1}.
 #' 
 #' @param subnet1 The matrix representing the first set of subnetworks
 #' @param subnet2 The matrix representing the second set of subnetworks