@@ -2,7 +2,7 @@ Package: KEGGlincs

 Type: Package

 Title: Visualize all edges within a KEGG pathway and overlay LINCS data

         [option]

-Version: 1.7.1

+Version: 1.7.2

 Date: 2016-06-02

 Author: Shana White

 Maintainer: Shana White <vandersm@mail.uc.edu>, Mario Medvedovic <medvedm@ucmail.uc.edu>

@@ -2,7 +2,6 @@

 export(KEGG_lincs)

 export(KL_compare)

-export(add_KEGG_drugs)

 export(add_edge_data)

 export(cyto_vis)

 export(edge_mapping_info)

@@ -10,10 +9,8 @@ export(expand_KEGG_edges)

 export(expand_KEGG_mappings)

 export(generate_mappings)

 export(get_KGML)

-export(get_drug_table)

 export(get_fisher_info)

 export(get_graph_object)

-export(grab_KO_data)

 export(keggerize_edges)

 export(node_mapping_info)

 export(overlap_info)

@@ -25,7 +22,6 @@ import(AnnotationDbi)

 import(KEGGREST)

 import(KOdata)

 import(RJSONIO)

-import(XML)

 import(hgu133a.db)

 import(httr)

 import(methods)

deleted file mode 100644

@@ -1,62 +0,0 @@

-#' Add edges from disease/drug tables  

-#' @description Expand edge mappings to include drugs/drug targets

-#' for selected pathway

-#' @param edges A data.frame object obtained by using the function `expand_kegg_edges`

-#' @param KEGG_mappings A data.frame object obtained by using the function `expand_kegg_mappings`

-#' @param kegg_drug_table A data.frame object obtained by using the function `get_drug_table`

-#' @return A data.frame object similar to the expanded edges data frame but with additional

-#' edges representing known drugs/drug targets

-#' @export

-#' @examples

-

-#' end_res_KGML <- get_KGML("hsa01522")

-#' end_res_KEGG_mappings <- expand_KEGG_mappings(end_res_KGML)

-#' end_res_edges <- expand_KEGG_edges(end_res_KGML, end_res_KEGG_mappings)

-

-#' end_res_drugs <- get_drug_table("hsa01522")

-

-#' edges_plus_kdrug <- add_KEGG_drugs(end_res_edges, end_res_KEGG_mappings, end_res_drugs)

-

-add_KEGG_drugs <- function(edges, KEGG_mappings, kegg_drug_table){

-

-    edges$u_ID <- paste0(edges$entry1accession,":", edges$entry2accession)

-    kegg_drug_table$u_ID <- paste0(kegg_drug_table$drug_KEGG_ID,":", kegg_drug_table$gene_id)

-    

-    drugs_to_add <- subset(kegg_drug_table, !kegg_drug_table$u_ID %in% edges$u_ID)

-    edges_to_add <- data.frame(

-       "edgeID" = seq(from = (1 + max(edges$edgeID)), to = (nrow(drugs_to_add) + max(edges$edgeID))), 

-       "entry1accession" = drugs_to_add$drug_KEGG_ID,

-       "entry2accession" = drugs_to_add$gene_id,

-       "entry1" = NA,

-       "entry2" = NA,

-       "type" = "PCrel",

-       "subtype1" = "from_kegg_drug",

-       "value" = "--",

-       "subtype2" = NA,

-       "value2" = NA,

-       "specific_subtype" = "from_kegg_drug",

-       "is_direct" = 1,

-       "entry1type" = "compound",

-       "entry2type" = "gene",

-       "entry1symbol" = drugs_to_add$drug_name,

-       "entry2symbol" = drugs_to_add$gene_symbol,

-       "u_ID" = drugs_to_add$u_ID,

-       stringsAsFactors = FALSE

-    )

-    for (i in 1:nrow(edges_to_add)){

-        edges_to_add$entry2[i] <- KEGG_mappings$entryID[KEGG_mappings$entryACCESSION == 

-                                                            edges_to_add$entry2accession[i]][1]

-        if (edges_to_add$entry1accession[i] %in% KEGG_mappings$entryACCESSION){

-            edges_to_add$entry1[i] <- KEGG_mappings$entryID[KEGG_mappings$entryACCESSION == 

-                                                                edges_to_add$entry1accession[i]][1]

-        }

-    }

-    # Decide whether or not to map to all nodes of gene on map

-    # for (i in 1:nrow(edges_to_add)){

-    #     edges_to_add$entry2[i] <- list(KEGG_mappings$entryID[KEGG_mappings$entryACCESSION == edges_to_add$entry2accession[i]])

-    # }

-    all_edges <- rbind(edges[, -c(17)], edges_to_add[, -c(17)])

-

-}

-

-#load("/opt/raid10/genomics/shana/KEGG_drug_targets/via_cts_convert/compound_cgs_KEGG_filtered.rda")

deleted file mode 100644

@@ -1,81 +0,0 @@

-#' Import disease/drug tables from KEGG 

-#' @description Get data tables for disease/drug information associated with 

-#' selected pathway

-#' @param pathwayid A KEGG pathway ID of the form "hsa12345" 

-#' (only human pathways currently)

-#' @return A data.frame object with either disease or drug information

-#' @import XML

-#' @export

-#' @examples

-#' RA_drug_table <- get_drug_table("hsa05323")

-

-get_drug_table <- function(pathwayid){

-    

-    raw_tabs <- GET(paste0("http://www.kegg.jp/kegg-bin/pathway_dd_list?map=",

-                           pathwayid))

-    

-    dd_table <- XML::readHTMLTable(rawToChar(raw_tabs$content),which = 4,

-                                   stringsAsFactors = F)

-    if (nrow(dd_table) > 0){

-        d_table <- subset(dd_table, 

-                          substring(dd_table[,1], 1, 1) == "D")

-        if(nrow(d_table) == 0){

-            warning("No associated drug targets in selected pathway")

-            return()

-        }

-        names(d_table) <- c("drug_KEGG_ID", "drug_name", "gene_target")

-        d_table$gene_target <- strsplit(d_table$gene_target, " ")

-        

-        for(i in 1:nrow(d_table)){

-            l <- length(unlist(d_table$gene_target[i]))

-            d_table$drug_KEGG_ID[i] <- list(rep(d_table$drug_KEGG_ID[i], l))

-            d_table$drug_name[i] <- list(rep(d_table$drug_name[i], l))

-        }

-        

-        long_drug <- data.frame("drug_KEGG_ID" = unlist(d_table$drug_KEGG_ID), 

-                                "drug_name" = unlist(d_table$drug_name), 

-                                "gene_target" = unlist(d_table$gene_target),

-                                stringsAsFactors = FALSE)

-        for (i in 1:nrow(long_drug)){

-            long_drug$gene_id[i] <- strsplit(long_drug$gene_target[i], 

-                                             "\\(")[[1]][1]

-            long_drug$gene_symbol[i] <- regmatches(long_drug$gene_target[i], 

-                                                   gregexpr("(?<=\\().*?(?=\\))", 

-                                                            long_drug$gene_target[i], 

-                                                            perl=TRUE))[[1]]

-        }

-        drops <- "gene_target"

-        d_table <- long_drug[, names(long_drug) != drops]

-        

-        return(d_table)

-    }

-    else {

-        warning("No drugs or diseases associated with selected pathway")

-        return()

-    }

-}

-#' @rdname get_drug_table 

-get_disease_table <- function(pathwayid){

-    

-    url <- paste0("http://www.kegg.jp/kegg-bin/pathway_dd_list?map=",

-                  pathwayid)

-    dd_table <- data.frame(

-        XML::readHTMLTable(url, header = TRUE, which = 4, as.data.frame = FALSE), 

-        stringsAsFactors = FALSE)

-    if (nrow(dd_table) > 0){

-        d_table <- subset(dd_table, 

-                          substring(dd_table$Disease.drug, 1, 1) == "H")

-        if(nrow(d_table) == 0){

-            warning("No diseases associated with selected pathway")

-            return()

-        }

-        return(d_table)

-    }

-    else {

-        warning("No drugs or diseases associated with selected pathway")

-        return()

-    }

-}

-

-#' @examples

-#' RA_disease_table <- get_disease_table("hsa05323")

deleted file mode 100644

@@ -1,56 +0,0 @@

-#' Quickly access LINCS L1000 CGS's for set of perturbagens (KO's)

-#' @description Translate raw CGS data to easy-to-use format

-#' @export

-#' @param cell_line Choose from the set of cell lines: 

-#' (A375,A549,ASC,HA1E,HCC515,HEK293T,HEKTE,HEPG2,HT29,MCF7,NCIH716,NPC,PC3,

-#' SHSY5Y,SKL,SW480,VCAP)  

-#' @param data_type Choose from data types: (100_full, 100_bing, 50_lm)

-#' @param pert_time Choose from (6,24,48,96,120,144,168)

-#' @param pathway_nodes Keep NA unless certain set of perturbagens is designated

-#' @return A data frame with conveniently formatted LINCS L100 CGS

-#' @examples 

-#' MCF_LM_50 <- grab_KO_data("MCF7")

-#' MCF_BING_100 <- grab_KO_data("MCF7", data_type = "100_bing")

-#' 

-grab_KO_data <- function(cell_line, pert_time = 96, data_type = "50_lm", 

-                         pathway_nodes = NA){

-    data("KO_data", envir = environment())

-    KO_data <- get("KO_data")

-    keeps <- c(names(KO_data[1:3]), paste0("up",data_type), 

-               paste0("dn",data_type))    

-    suppressWarnings(    

-        if(is.na(pathway_nodes)){

-            KO_by_CT <- KO_data[KO_data$pert_time == pert_time & 

-                                    KO_data$cell_id == cell_line, keeps]

-        }

-    )

-    suppressWarnings(

-        if(!is.na(pathway_nodes)){

-            KO_by_CT <- KO_data[KO_data$pert_time == pert_time & 

-                                    KO_data$cell_id == cell_line &

-                                    KO_data$pert_desc %in% pathway_nodes, keeps]

-        }

-    )

-    names(KO_by_CT)[c(4,5)] <- c("up", "down")

-    KO_by_CT <- KO_by_CT[,c(2,4:5)]

-    data("conversion_key")

-    data("L1000_LM_genes")

-    

-    for (i in 1:nrow(KO_by_CT)){

-        

-        KO_by_CT$up_SYMBOL[i] <- 

-            list(conversion_key$pr_gene_symbol[

-                which(conversion_key$pr_id %in% 

-                unlist(strsplit(KO_by_CT$up[i], ";")))])

-        KO_by_CT$down_SYMBOL[i] <-

-            list(conversion_key$pr_gene_symbol[

-                which(conversion_key$pr_id %in% 

-                unlist(strsplit(KO_by_CT$down[i], ";")))])

-        KO_by_CT$up_count[i] <- length(unlist(KO_by_CT$up_SYMBOL[i]))

-        KO_by_CT$down_count[i] <- length(unlist(KO_by_CT$down_SYMBOL[i]))

-    }

-    KO_by_CT <- KO_by_CT[,c(1,4,5)]

-    names(KO_by_CT) <- c("knockout", "up", "down")

-    rownames(KO_by_CT) <- KO_by_CT$knockout

-    return(KO_by_CT)

-}

\ No newline at end of file

deleted file mode 100644

Binary files a/data/L1000_LM_genes.rda and /dev/null differ

deleted file mode 100644

Binary files a/data/conversion_key.rda and /dev/null differ

deleted file mode 100644

@@ -1,30 +0,0 @@

-% Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/add_KEGG_drugs.R

-\name{add_KEGG_drugs}

-\alias{add_KEGG_drugs}

-\title{Add edges from disease/drug tables}

-\usage{

-add_KEGG_drugs(edges, KEGG_mappings, kegg_drug_table)

-}

-\arguments{

-\item{edges}{A data.frame object obtained by using the function `expand_kegg_edges`}

-

-\item{KEGG_mappings}{A data.frame object obtained by using the function `expand_kegg_mappings`}

-

-\item{kegg_drug_table}{A data.frame object obtained by using the function `get_drug_table`}

-}

-\value{

-A data.frame object similar to the expanded edges data frame but with additional

-edges representing known drugs/drug targets

-}

-\description{

-Expand edge mappings to include drugs/drug targets

-for selected pathway

-}

-\examples{

-end_res_KGML <- get_KGML("hsa01522")

-end_res_KEGG_mappings <- expand_KEGG_mappings(end_res_KGML)

-end_res_edges <- expand_KEGG_edges(end_res_KGML, end_res_KEGG_mappings)

-end_res_drugs <- get_drug_table("hsa01522")

-edges_plus_kdrug <- add_KEGG_drugs(end_res_edges, end_res_KEGG_mappings, end_res_drugs)

-}

deleted file mode 100644

@@ -1,25 +0,0 @@

-% Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/get_dd_tables.R

-\name{get_drug_table}

-\alias{get_drug_table}

-\alias{get_disease_table}

-\title{Import disease/drug tables from KEGG}

-\usage{

-get_drug_table(pathwayid)

-

-get_disease_table(pathwayid)

-}

-\arguments{

-\item{pathwayid}{A KEGG pathway ID of the form "hsa12345" 

-(only human pathways currently)}

-}

-\value{

-A data.frame object with either disease or drug information

-}

-\description{

-Get data tables for disease/drug information associated with 

-selected pathway

-}

-\examples{

-RA_drug_table <- get_drug_table("hsa05323")

-}

deleted file mode 100644

@@ -1,31 +0,0 @@

-% Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/grab_KO_data.R

-\name{grab_KO_data}

-\alias{grab_KO_data}

-\title{Quickly access LINCS L1000 CGS's for set of perturbagens (KO's)}

-\usage{

-grab_KO_data(cell_line, pert_time = 96, data_type = "50_lm",

-  pathway_nodes = NA)

-}

-\arguments{

-\item{cell_line}{Choose from the set of cell lines: 

-(A375,A549,ASC,HA1E,HCC515,HEK293T,HEKTE,HEPG2,HT29,MCF7,NCIH716,NPC,PC3,

-SHSY5Y,SKL,SW480,VCAP)}

-

-\item{pert_time}{Choose from (6,24,48,96,120,144,168)}

-

-\item{data_type}{Choose from data types: (100_full, 100_bing, 50_lm)}

-

-\item{pathway_nodes}{Keep NA unless certain set of perturbagens is designated}

-}

-\value{

-A data frame with conveniently formatted LINCS L100 CGS

-}

-\description{

-Translate raw CGS data to easy-to-use format

-}

-\examples{

-MCF_LM_50 <- grab_KO_data("MCF7")

-MCF_BING_100 <- grab_KO_data("MCF7", data_type = "100_bing")

-

-}