Mercurial > repos > mingchen0919 > aurora_deseq2_site
comparison DESeq_04.Rmd @ 0:6f94b4b9de44 draft
planemo upload
author | mingchen0919 |
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date | Tue, 27 Feb 2018 23:57:53 -0500 |
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1 --- | |
2 output: html_document | |
3 --- | |
4 | |
5 ```{r setup, include=FALSE, warning=FALSE, message=FALSE} | |
6 knitr::opts_chunk$set( | |
7 echo = as.logical(opt$X_e), | |
8 error = TRUE | |
9 ) | |
10 ``` | |
11 | |
12 | |
13 | |
14 # Sample distance on variance stabilized data {.tabset} | |
15 | |
16 ## `rlog` Stabilizing transformation | |
17 | |
18 ```{r} | |
19 rld = rlog(dds, blind = FALSE) | |
20 datatable(head(assay(rld), 100), style="bootstrap", | |
21 class="table-condensed", options = list(dom = 'tp', scrollX = TRUE)) | |
22 ``` | |
23 | |
24 ## Sample distance | |
25 | |
26 ```{r} | |
27 sampleDists <- dist(t(assay(rld))) | |
28 sampleDists | |
29 ``` |