Mercurial > repos > mingchen0919 > aurora_deseq2

changeset 3:caae0a188548 draft

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add deseq2 package
author mingchen0919
date Thu, 08 Mar 2018 21:03:01 -0500
parents 405d8fa2f560
children f4b8887aac56
files deseq2.Rmd deseq2.sh deseq2.xml deseq2_render.R spec.txt
diffstat 5 files changed, 57 insertions(+), 47 deletions(-) [+]
line wrap: on
line diff
--- a/deseq2.Rmd	Thu Mar 08 20:13:30 2018 -0500
+++ b/deseq2.Rmd	Thu Mar 08 21:03:01 2018 -0500
@@ -1,29 +1,31 @@
 ---
-title: 'HTML report title'
-output:
-    html_document:
-      number_sections: true
-      toc: true
-      theme: cosmo
-      highlight: tango
+title: 'DESeq2 Analysis'
+output: html_document
 ---
 
 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
 knitr::opts_chunk$set(
-  echo = as.logical(), 
+  echo = as.logical(opt$X_e), 
   error = TRUE
 )
 ```
 
 
-# Code for computational analysis
-
-```{r 'step 1'}
+## DESeq2 analysis
 
-```
-
-```{r 'ste[ 2'}
-
+```{r}
+coldata = read.csv(opt$X_B, row.names = 1, header = TRUE)
+dds = DESeqDataSetFromMatrix(countData = count_data,
+                             colData = coldata,
+                             design = expression(opt$X_C))
+dds = DESeq(dds, test = opt$X_G, fitType = opt$X_H)
 ```
 
 
+## Results
+
+```{r}
+res = results(dds, contrast = c(opt$X_D, opt$X_E, opt$X_F), alpha = opt$X_I)
+res
+```
+
--- a/deseq2.sh	Thu Mar 08 20:13:30 2018 -0500
+++ b/deseq2.sh	Thu Mar 08 21:03:01 2018 -0500
@@ -6,12 +6,13 @@
   -s $sink_message
   -t '${__tool_directory__}' 
   
-  -A $count_data
-  -B $column_data
-  -C $design_formula
-  -D $treatment_name
-  -E $treated
-  -F $untreated
-  -G $test_type
-  -H $fit_type
-  -I $alpha
\ No newline at end of file
+  -A '$count_data'
+  -B '$column_data'
+  -C '$design_formula'
+  -D '$treatment_name'
+  -E '$treated'
+  -F '$untreated'
+  -G '$test_type'
+  -H '$fit_type'
+  -I '$alpha'
+  -J '$significant_genes'
\ No newline at end of file
--- a/deseq2.xml	Thu Mar 08 20:13:30 2018 -0500
+++ b/deseq2.xml	Thu Mar 08 21:03:01 2018 -0500
@@ -19,15 +19,15 @@
   -s $sink_message
   -t '${__tool_directory__}' 
   
-  -A $count_data
-  -B $column_data
-  -C $design_formula
-  -D $treatment_name
-  -E $treated
-  -F $untreated
-  -G $test_type
-  -H $fit_type
-  -I $alpha]]></command>
+  -A '$count_data'
+  -B '$column_data'
+  -C '$design_formula'
+  -D '$treatment_name'
+  -E '$treated'
+  -F '$untreated'
+  -G '$test_type'
+  -H '$fit_type'
+  -I '$alpha']]></command>
     <inputs>
         <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false"
                label="Display analysis code in report?"/>
--- a/deseq2_render.R	Thu Mar 08 20:13:30 2018 -0500
+++ b/deseq2_render.R	Thu Mar 08 21:03:01 2018 -0500
@@ -17,12 +17,25 @@
 
 
 #------------get arguments into R--------------------
-library(dplyr)
-getopt_specification_matrix(extract_short_flags('deseq2.xml')) %>%
-  write.table(file = 'spec.txt', sep = ',', row.names = FALSE, col.names = TRUE, quote = FALSE)
+# library(dplyr)
+# getopt_specification_matrix(extract_short_flags('deseq2.xml')) %>%
+#   write.table(file = 'spec.txt', sep = ',', row.names = FALSE, col.names = TRUE, quote = FALSE)
 
 
-spec_matrix = as.matrix()
+spec_matrix = as.matrix(
+  data.frame(stringsAsFactors=FALSE,
+              long_flags = c("X_e", "X_o", "X_d", "X_s", "X_t", "X_A", "X_B",
+                             "X_C", "X_D", "X_E", "X_F", "X_G", "X_H", "X_I"),
+             short_flags = c("e", "o", "d", "s", "t", "A", "B", "C", "D", "E",
+                             "F", "G", "H", "I", "J"),
+     argument_mask_flags = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
+                             1L, 1L),
+         data_type_flags = c("character", "character", "character", "character",
+                             "character", "character", "character", "character",
+                             "character", "character", "character", "character",
+                             "character", "character", "character")
+  )
+)
 opt = getopt(spec_matrix)
 #----------------------------------------------------
 
@@ -35,16 +48,16 @@
 #---------- often used variables ----------------
 # OUTPUT_DIR: path to the output associated directory, which stores all outputs
 # TOOL_DIR: path to the tool installation directory
-OUTPUT_DIR = ''
-TOOL_DIR =   ''
-RMD_NAME = ''
+OUTPUT_DIR = opt$X_d
+TOOL_DIR =   opt$X_t
+RMD_NAME = 'deseq2.Rmd'
 OUTPUT_REPORT = opt$X_o
 
 # create the output associated directory to store all outputs
 dir.create(OUTPUT_DIR, recursive = TRUE)
 
 #-----------------render Rmd--------------
-render(paste0(TOOL_DIR, RMD_NAME, sep = '/'), output_file = OUTPUT_REPORT)
+render(paste0(TOOL_DIR, '/', RMD_NAME), output_file = OUTPUT_REPORT)
 #------------------------------------------
 
 #==============the end==============
--- a/spec.txt	Thu Mar 08 20:13:30 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-long_flags,short_flags,argument_mask_flags,data_type_flags
-X_e,e,1,character
-X_o,o,1,character
-X_d,d,1,character
-X_s,s,1,character
-X_t,t,1,character