Initialise repo

DESCRIPTION

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+Package: BoolTraineR
+Type: Package
+Title: Tools For Training and Analysing Asynchronous Boolean Models
+Version: 1.0.1
+Date: 2015-10-22
+Author: Chee Yee Lim
+Maintainer: Chee Yee Lim <cyl49@cam.ac.uk> <cheeyee.lim@gmail.com>
+Description: This package contains tools for Boolean model manipulation, as well as the search for the best Boolean model.
+Depends: 
+    R (>= 3.0.3),
+    methods
+Imports:
+    parallel,
+    Rcpp (>= 0.11.4),
+    foreach (>= 1.4.1),
+    doParallel (>= 1.0.8),
+    poweRlaw (>= 0.30.0),
+    MASS (>= 7.3-44),
+    diptest (>= 0.75-7)
+LinkingTo: Rcpp
+License: GPL-3
+LazyData: true

NAMESPACE

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+# Generated by roxygen2 (4.1.1): do not edit by hand
+
+export(BoolModel)
+export(amat_to_bm)
+export(bin_to_real)
+export(bm_to_amat)
+export(bm_to_df)
+export(calc_mscore)
+export(calc_roc)
+export(check_bmodel)
+export(compress_bmodel)
+export(decompress_bmodel)
+export(df_to_bm)
+export(equi_model)
+export(gen_randata)
+export(gen_randata_bn)
+export(gen_two_rmodel)
+export(gen_two_rmodel_dag)
+export(get_encodings)
+export(grow_bmodel)
+export(initialise_data)
+export(initialise_model)
+export(initialise_raw_data)
+export(model_consensus)
+export(model_dist)
+export(model_setdiff)
+export(model_train)
+export(outcyto_model)
+export(outcyto_stategraph)
+export(outgenysis_model)
+export(param_bimodal)
+export(printBM)
+export(simulate_model)
+export(unique_raw_data)
+export(validate_adjmat)
+export(writeBM)
+exportClasses(BoolModel)
+import(doParallel)
+import(foreach)
+import(methods)
+import(parallel)
+importFrom(Rcpp,evalCpp)
+importFrom(Rcpp,sourceCpp)
+useDynLib(BoolTraineR)

R/RcppExports.R

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+# This file was generated by Rcpp::compileAttributes
+# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
+
+#' @title Find a match between two data frames.
+#' 
+#' @description
+#' (&&&Not for public use&&&)This function finds a match between two df of states. Used in match_state(). Return an row index vector indicating which row of mstate matches the rows in xstate.
+#' 
+#' @param mstate data frame. It should be a state(row) x gene(column) df.
+#' @param xstate data frame. It should be a state(row) x gene(column) df.
+match_state_loop <- function(mstate, xstate) {
+    .Call('BoolTraineR_match_state_loop', PACKAGE = 'BoolTraineR', mstate, xstate)
+}
+
+#' @title Calculating pairwise scores between model and data states.
+#' 
+#' @description
+#' This function calculates the pairwise scores between each row of model and data states. The score is calculated using a custom binary distance measure.
+#' 
+#' @param x_df matrix. It should be numerical matrix of model states.
+#' @param y_df matrix. It should be numerical matrix of data states.
+rcpp_man_dist <- function(x_df, y_df) {
+    .Call('BoolTraineR_rcpp_man_dist', PACKAGE = 'BoolTraineR', x_df, y_df)
+}
+
+#' @title Calculating Hamming pairwise scores between model and data states.
+#' 
+#' @description
+#' This function calculates the pairwise scores between each row of model and data states. The score is calculated using a custom binary distance measure.
+#' 
+#' @param x_df matrix. It should be logical matrix of model states.
+#' @param y_df matrix. It should be logical matrix of data states.
+rcpp_ham_dist <- function(x_df, y_df) {
+    .Call('BoolTraineR_rcpp_ham_dist', PACKAGE = 'BoolTraineR', x_df, y_df)
+}
+
+#' @title Inner core for m_score()
+#' 
+#' @description
+#' This function takes in a df with columns ranked wrt each row, and try to assign each row to a unique column without repetition.
+#' 
+#' @param x_df matrix. Matrix with columns ranked wrt each row.
+rcpp_m_score <- function(x_df) {
+    .Call('BoolTraineR_rcpp_m_score', PACKAGE = 'BoolTraineR', x_df)
+}
+
+#' @title Calculating validation scores between two adjacency matrices
+#' 
+#' @description
+#' This function calculates the validation scores between two adjacency matrices.
+#' 
+#' @param inf_mat matrix. It should be adjacency matrix of inferred network.
+#' @param true_mat matrix. It should be adjacency matrix of true network.
+rcpp_validate <- function(inf_mat, true_mat) {
+    .Call('BoolTraineR_rcpp_validate', PACKAGE = 'BoolTraineR', inf_mat, true_mat)
+}
+
+#' @title Simulate a Boolean model.
+#' 
+#' @description
+#' (&&&Not for public use&&&)This function simulates the Boolean model using an initial state. For use within simulate_model(). Returns a matrix of full asynchronous state space.
+#' 
+#' @param bmodel list. A list of 4 lists created by decreate_model().
+#' @param fstate data frame. It must have been initialised by initialise_data(), and has gene names as column names. Must contain only 1 row.
+#' @param verbose logical. Indicates whether to output progress.
+rcpp_simulate <- function(bmodel, fstate, verbose = FALSE) {
+    .Call('BoolTraineR_rcpp_simulate', PACKAGE = 'BoolTraineR', bmodel, fstate, verbose)
+}
+

R/boolmodel_class.R

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+#' @title An S4 class to represent a Boolean Model
+#' 
+#' @description
+#' This class represents Boolean Model in a S4 BoolModel object.
+#' 
+#' @field target character vector. It should contain gene symbols.
+#' @field targer_var character vector. It should contain the internal representation of gene variables, in the form of "v[0-9]+s"
+#' @field rule_act list of character vectors. Each element in the list should contain the activating gene variables for a particular target gene.
+#' @field rule_inh list of character vectors. Each element in the list should contain the inhibiting gene variables for a particular target gene.
+#' 
+#' @export BoolModel
+#' @exportClass BoolModel
+BoolModel = setClass('BoolModel',
+                       slots=c(target='character', target_var='character', 
+                               rule_act='list', rule_inh='list')
+                     )
+

R/booltrainer.R

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+#' @title BoolTraineR: A package for studying asynchronous Boolean models
+#' 
+#' @description
+#' This package contains tools for Boolean model manipulation, as well as the search for the best Boolean model.
+#' 
+#' @docType package
+#' @name BoolTraineR
+NULL
+
+## All the Roxygen codes below are for generating the correct NAMESPACE file.
+#' @import methods
+#' @import parallel
+#' @import foreach
+#' @import doParallel
+NULL
+
+#' @useDynLib BoolTraineR
+#' @importFrom Rcpp sourceCpp evalCpp
+NULL