updated docs

elswob · Jul 28, 2015 · cbaceb1 · cbaceb1
1 parent 19d6110
commit cbaceb1
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Showing 4 changed files with 10 additions and 5 deletions.
diff --git a/R/subtype_functions.R b/R/subtype_functions.R
@@ -538,6 +538,7 @@ run_scmgene=function(){
 #' @param short A short name for the analysis
 #' @param pamCC (default=0.75) Correlation confidence cutoff used to assign a PAM50 subtype as Low Confidence (LC)
 #' @param samp_num (default=5) Minumum percentage of samples containing value > 0 per gene
+#' @param remove_lc (default TRUE) Remove the samples with a corerrelation confidence less than pamCC
 run_basalt=function(outDir,inputFile,short,pamCC=0.75,samp_num=5,remove_lc=TRUE){
   outDir<<-outDir
   inputFile<<-inputFile

diff --git a/man/cor_plot.Rd b/man/cor_plot.Rd
@@ -4,13 +4,15 @@
 \alias{cor_plot}
 \title{Generate the PAM50 correlation coefficient plots}
 \usage{
-cor_plot(p, id, name)
+cor_plot(p, id, name, outDir)
 }
 \arguments{
 \item{id}{The ID of the samples to extract}
 
 \item{name}{The name to represent the samples}
 
+\item{outDir}{The output directory}
+
 \item{p50}{The PAM50 results text file}
 }
 \description{

diff --git a/man/run_basal.Rd → man/run_basalt.Rd b/man/run_basal.Rd → man/run_basalt.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_basal}
-\alias{run_basal}
+\name{run_basalt}
+\alias{run_basalt}
 \title{Run the subtype analysis}
 \usage{
-run_basal(outDir, inputFile, short, pamCC = 0.75, samp_num = 5,
+run_basalt(outDir, inputFile, short, pamCC = 0.75, samp_num = 5,
   remove_lc = TRUE)
 }
 \arguments{
@@ -17,6 +17,8 @@ run_basal(outDir, inputFile, short, pamCC = 0.75, samp_num = 5,
 \item{pamCC}{(default=0.75) Correlation confidence cutoff used to assign a PAM50 subtype as Low Confidence (LC)}
 
 \item{samp_num}{(default=5) Minumum percentage of samples containing value > 0 per gene}
+
+\item{remove_lc}{(default TRUE) Remove the samples with a corerrelation confidence less than pamCC}
 }
 \description{
 Run the subtype analysis

diff --git a/man/setup.Rd b/man/setup.Rd
@@ -4,7 +4,7 @@
 \alias{setup}
 \title{Set up the analysis}
 \usage{
-setup(outDir, inputFile, short, samp_num, pamCC)
+setup(outDir, inputFile, short, samp_num, pamCC, remove_lc)
 }
 \description{
 Set up the analysis