Mercurial > repos > mingchen0919 > aurora_deseq2_site
comparison DESeq_02.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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-1:000000000000 | 0:6f94b4b9de44 |
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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 # Pre-filtering the dataset. | |
15 | |
16 We can remove the rows that have 0 or 1 count to reduce object size and increase the calculation speed. | |
17 | |
18 * Number of rows before pre-filtering | |
19 ```{r} | |
20 nrow(dds) | |
21 ``` | |
22 | |
23 * Number of rows after pre-filtering | |
24 ```{r} | |
25 dds = dds[rowSums(counts(dds)) > 1, ] | |
26 nrow(dds) | |
27 ``` |