@@ -13,6 +13,7 @@ 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)

new file mode 100644

@@ -0,0 +1,57 @@

+#' 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 edge_id The numeric value for the edge_id

+#' @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

new file mode 100644

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

new file mode 100644

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

new file mode 100644

@@ -0,0 +1,33 @@

+% 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}

+

+\item{edge_id}{The numeric value for the edge_id}

+}

+\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")

+

+}

new file mode 100644

@@ -0,0 +1,97 @@

+#!/usr/bin/env bash

+

+# This script should be run after cloning, it will update the remote

+# information so that git svn commands work properly for both the master and

+# release branches.

+

+set -eou pipefail

+IFS=$'\n\t'

+

+set +u

+package=$1

+

+# otherwise use the default repo name

+if [ -z "$package" ];then

+  package=$(git remote -v | perl -ne 'if (m!/([^/]+?)(?:.git)?\s!) { print $1; exit}')

+fi

+set -u

+

+base_url="https://hedgehog.fhcrc.org/bioconductor/"

+

+is_mirror_clone () {

+  git remote show origin | grep -i -q bioconductor-mirror

+  return $?

+}

+

+add_release_tracking () {

+  local branch=$1

+  shift

+  local remote=$1

+  shift

+  for release_branch in $@; do

+    svn_branch=$(echo $release_branch | perl -ne 'if (/release-(\d+)\.(\d+)/) { print "RELEASE_$1_$2"; }')

+    svn_url="$base_url/branches/$svn_branch/madman/Rpacks/$package"

+    git config --add svn-remote.$release_branch.url $svn_url

+    git config --add svn-remote.$release_branch.fetch :refs/remotes/git-svn-$release_branch

+    git update-ref refs/remotes/git-svn-$release_branch refs/$remote/$release_branch

+  done

+}

+

+add_branch () {

+  set +eu

+  local local_branch=$1

+  local remote_branch=${2-$local_branch}

+  if ! git branch --track $local_branch bioc/$remote_branch  2>/dev/null 1>&2; then

+    1>&2 cat <<END

+$local_branch already exists, create a custom branch to track bioc/$remote_branch with

+  \`git branch --track NEW_NAME bioc/$remote_branch\`

+END

+  fi

+}

+

+if is_mirror_clone; then

+    git checkout master

+    git svn init "$base_url/trunk/madman/Rpacks/$package"

+    git update-ref refs/remotes/git-svn refs/remotes/origin/master

+    git svn rebase

+    git remote add bioc https://github.com/Bioconductor-mirror/${package}.git

+    git fetch bioc 2>/dev/null 1>&2

+

+    release_branches=$(git branch -r | perl -ne 'if (m!origin/(release-.*)!) { print $1, "\n" }')

+    for release_branch in ${release_branches[@]}; do

+      add_branch $release_branch

+    done

+

+    add_release_tracking origin heads $release_branches

+

+    cat <<\END

+Commit to git as normal, when you want to push your commits to svn

+  1. `git svn rebase` to get the latest SVN changes.

+  2. `git svn dcommit --add-author-from` to commit your changes to SVN.

+END

+

+else

+    git remote add bioc "https://github.com/Bioconductor-mirror/${package}.git"

+    git fetch bioc 2>/dev/null 1>&2

+    git config --add svn-remote.devel.url "$base_url/trunk/madman/Rpacks/$package"

+    git config --add svn-remote.devel.fetch :refs/remotes/git-svn-devel

+    git update-ref refs/remotes/git-svn-devel refs/remotes/bioc/master

+

+    release_branches=$(git branch -r | perl -ne 'if (m!bioc/(release-.*)!) { print $1, "\n" }')

+    add_release_tracking bioc remotes/bioc $release_branches

+

+    for release_branch in ${release_branches[@]}; do

+      add_branch $release_branch

+    done

+    add_branch devel master

+    cat <<\END

+Commit to git as normal, when you want to push your commits to svn

+  1. `git checkout devel` to switch to the devel branch. (use release-X.X for

+        release branches)

+  2. `git svn rebase` to get the latest SVN changes.

+  3. `git merge master --log` to merge your changes from the master branch

+        or skip this step and work directly on the current branch.

+  4. `git svn dcommit --add-author-from` to sync and commit

+        your changes to svn.

+END

+fi