Mercurial > repos > mingchen0919 > rmarkdown_deseq2_count_matrix

comparison rmarkdown_deseq2_count_matrix.Rmd @ 0:c1f718dd6c7a draft

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planemo upload
author mingchen0919
date Sat, 30 Dec 2017 00:25:38 -0500
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children 629323b5fc0c
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-1:000000000000 0:c1f718dd6c7a
1 ---
2 title: 'DESeq2 analysis'
3 output:
4 html_document:
5 number_sections: true
6 toc: true
7 theme: cosmo
8 highlight: tango
9 ---
10
11 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
12 knitr::opts_chunk$set(
13 echo = opt$echo,
14 error = TRUE
15 )
16 ```
17
18
19 ## User input
20
21 ```{r 'user input'}
22 df = data.frame(name = names(opt)[-1],
23 value = unlist(opt))
24 df
25 ```
26
27
28 ## Count Matrix
29
30 ```{r 'count matrix'}
31 count_data = read.table(opt$count_data)
32 head(count_data, 10)
33 ```
34
35 ```{r 'ste[ 2'}
36
37 ```
38
39