bug fixes

elswob · Jul 10, 2015 · 8d1e71f · 8d1e71f
1 parent ae58f70
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diff --git a/R/subtype_functions.R b/R/subtype_functions.R
@@ -1,34 +1,17 @@
 ### Ben Elsworth July 2015
 
-# source("http://bioconductor.org/biocLite.R")
-# biocIfnot <- function (packageName){
-#   if (!(require(packageName, character.only=TRUE))) biocLite(packageName)
-# }
-# installifnot <- function (packageName){
-#   if (!(require(packageName)))
-#     install.packages(packageName, dependencies=TRUE, repos="http://cran.rstudio.com/")
-# }
-#installifnot("ggplot2")
-#installifnot("gplots")
-#installifnot("heatmap.plus")
-#installifnot("GMD")
-#installifnot("reshape")
-#biocIfnot("org.Hs.eg.db")
-#biocIfnot("genefu")
-#biocIfnot("ctc")
-
-library(ggplot2)
-library(gplots)
-library(org.Hs.eg.db)
-library(genefu)
-library(heatmap.plus)
-library(reshape)
-library(RColorBrewer)
-#library(GMD)
-
 ####################################################################
 #' Set up the analysis
 setup=function(){
+  #load libraries
+  library(ggplot2)
+  library(gplots)
+  library(org.Hs.eg.db)
+  library(genefu)
+  library(heatmap.plus)
+  library(reshape)
+  library(RColorBrewer)
+
   #load PAM50 genes
   p50<<-c('ACTR3B','ANLN','BAG1','BCL2','BIRC5','BLVRA','CCNB1','CCNE1','CDC20','CDC6','CDCA1','CDH3','CENPF','CEP55','CXXC5','EGFR','ERBB2','ESR1','EXO1','FGFR4','FOXA1','FOXC1','GPR160','GRB7','KIF2C','KNTC2','KRT14','KRT17','KRT5','MAPT','MDM2','MELK','MIA','MKI67','MLPH','MMP11','MYBL2','MYC','NAT1','ORC6L','PGR','PHGDH','PTTG1','RRM2','SFRP1','SLC39A6','TMEM45B','TYMS','UBE2C','UBE2T')
 

diff --git a/README.md b/README.md
@@ -6,29 +6,24 @@ Runs PAM50 and SCMGENE subtype methods on log2 expression data
 
 ### Requirements
 
-A file with samplenames as column IDs, gene symbols as row IDs and log2 expression data. Any gene symbol can be present in the file as long as ESR1 and ERBB2 are there, otherwise PAM50 won't work.
+A tab delimited file with samplenames as column IDs, gene symbols as row IDs and log2 expression data. Any gene symbol can be present in the file as long as ESR1 and ERBB2 are there, otherwise PAM50 won't work.
 
 ```
-Symbol    EFM192A	EVSAT	MDAMB453	MDAMB231	MDAMB468	BT549	CAL851	EFM19
-A1BG	    8.315511	5.454009	7.822566	6.140037	5.111359	7.599171	5.173046	6.038426
-A2M	      4.107914	3.714508	3.907026	4.059009	7.406219	3.973131	4.741874	3.801728
-NAT1	    8.914029	8.343696	9.054734	8.80809	8.708712	7.315499	8.805189	6.833612
-NAT2	    6.564016	4.953733	4.763946	4.644254	4.364252	4.228607	5.419792	4.522074
+Hugo_symbol	EFM192A	EVSAT	MDAMB453	MDAMB231	MDAMB468	BT549	CAL851	EFM19
+A1BG	8.315511	5.454009	7.822566	6.140037	5.111359	7.599171	5.173046	6.038426
+A2M	4.107914	3.714508	3.907026	4.059009	7.406219	3.973131	4.741874	3.801728
+NAT1	8.914029	8.343696	9.054734	8.80809	8.708712	7.315499	8.805189	6.833612
+NAT2	6.564016	4.953733	4.763946	4.644254	4.364252	4.228607	5.419792	4.522074
 SERPINA3	8.339674	5.361677	4.422622	4.641157	9.53551	5.258785	11.69059	8.127704
-AADAC	    4.326528	4.037927	3.680285	3.766857	3.94583	3.694712	4.694278	3.882659
-AAMP	    9.266102	10.43423	9.745142	8.790493	9.474694	8.564627	8.914895	9.234852
-AANAT	    4.118585	4.168364	3.84862	3.839901	4.013059	4.515908	3.721725	3.903788
-AARS	    10.73831	10.82067	10.40384	9.457173	10.26427	10.38802	10.48933	9.772005
+AADAC	4.326528	4.037927	3.680285	3.766857	3.94583	3.694712	4.694278	3.882659
+AAMP	9.266102	10.43423	9.745142	8.790493	9.474694	8.564627	8.914895	9.234852
+AANAT	4.118585	4.168364	3.84862	3.839901	4.013059	4.515908	3.721725	3.903788
+AARS	10.73831	10.82067	10.40384	9.457173	10.26427	10.38802	10.48933	9.772005
 ``` 
 
 ### Installation
 
-```
-install.packages("devtools")
-devtools::install_github("elswob/BASAL")
-```
 Install some libraries
-
 ```
 library(ggplot2)
 library(gplots)
@@ -39,6 +34,13 @@ library(reshape)
 library(RColorBrewer)
 ```
 
+Install and load BASAL
+```
+install.packages("devtools")
+devtools::install_github("elswob/BASAL")
+libary(BASAL)
+```
+
 ### To run
 
 Need three arguements:

diff --git a/man/cor_plot.Rd b/man/cor_plot.Rd
@@ -4,14 +4,14 @@
 \alias{cor_plot}
 \title{Generate the PAM50 correlation coefficient plots}
 \usage{
-cor_plot(p50, id, name)
+cor_plot(p, id, name)
 }
 \arguments{
-\item{p50}{The PAM50 results text file}
-
 \item{id}{The ID of the samples to extract}
 
 \item{name}{The name to represent the samples}
+
+\item{p50}{The PAM50 results text file}
 }
 \description{
 Generate the PAM50 correlation coefficient plots

diff --git a/man/run_analysis.Rd → man/run_basal.Rd b/man/run_analysis.Rd → man/run_basal.Rd
@@ -1,10 +1,10 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/subtype_functions.R
-\name{run_analysis}
-\alias{run_analysis}
+\name{run_basal}
+\alias{run_basal}
 \title{Run the subtype analysis}
 \usage{
-run_analysis(d, f, s)
+run_basal(d, f, s)
 }
 \arguments{
 \item{inputDir}{The directory containing the input file}

diff --git a/pam50_data/scmgene/scmgene_classif.pdf b/pam50_data/scmgene/scmgene_classif.pdf
diff --git a/pam50_data/scmgene/scmgene_fit_EXPO.pdf b/pam50_data/scmgene/scmgene_fit_EXPO.pdf
diff --git a/pam50_data/scmgene/scmgene_model_EXPO.csv b/pam50_data/scmgene/scmgene_model_EXPO.csv