Browse code

update documentation for newer roxygen version

From: vandersm <vandersm@mail.uc.edu>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/KEGGlincs@127888 bc3139a8-67e5-0310-9ffc-ced21a209358

Shana White authored on 30/03/2017 20:47:47
Showing1 changed files
... ...
@@ -31,4 +31,3 @@ p53_KEGG_mappings <- expand_KEGG_mappings(p53_KGML)
31 31
 
32 32
 path_genes_by_cell_type(p53_KEGG_mappings)
33 33
 }
34
-
Browse code

Adding KEGGlincs, flowPloidy, MAST, PathoStat, matter, MoonlightR, psichomics, anamiR, MutationalPatterns, HelloRanges, crisprseekplus, annotatr, meshes

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/KEGGlincs@122278 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 12/10/2016 17:44:52
Showing1 changed files
1 1
new file mode 100644
... ...
@@ -0,0 +1,34 @@
1
+% Generated by roxygen2: do not edit by hand
2
+% Please edit documentation in R/path_genes_by_cell_type.R
3
+\name{path_genes_by_cell_type}
4
+\alias{path_genes_by_cell_type}
5
+\title{See how many pathway gene knock-outs are available from data}
6
+\usage{
7
+path_genes_by_cell_type(KEGG_mappings, pert_time = 96, get_KOs = FALSE,
8
+  generate_plot = TRUE)
9
+}
10
+\arguments{
11
+\item{KEGG_mappings}{KEGG_mappings The data.frame object generated by the 
12
+function expand_KEGG_mappings}
13
+
14
+\item{pert_time}{Choose from (6,24,48,96,120,144,168)}
15
+
16
+\item{get_KOs}{Logical indicator to have data frame returned}
17
+
18
+\item{generate_plot}{Logical indicator to generate histogram}
19
+}
20
+\value{
21
+A plot depicting percentage of pathway genes knocked-out by 
22
+cell line and a data frame object listing the genes [by cell line]
23
+}
24
+\description{
25
+Check quantity of data across cell lines available from LINCS
26
+ corresponding to the pathway of interest
27
+}
28
+\examples{
29
+p53_KGML <- get_KGML("hsa04115")
30
+p53_KEGG_mappings <- expand_KEGG_mappings(p53_KGML)
31
+
32
+path_genes_by_cell_type(p53_KEGG_mappings)
33
+}
34
+