Mercurial > repos > mingchen0919 > aurora_deseq2_site
comparison DESeq_results_01.Rmd @ 0:6f94b4b9de44 draft
planemo upload
| author | mingchen0919 |
|---|---|
| date | Tue, 27 Feb 2018 23:57:53 -0500 |
| parents | |
| children |
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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 ```{r eval=TRUE} | |
| 14 # Import workspace | |
| 15 # fcp = file.copy(opt$X_W, "deseq.RData") | |
| 16 load(opt$X_W) | |
| 17 ``` | |
| 18 | |
| 19 # Results {.tabset} | |
| 20 | |
| 21 ## Result table | |
| 22 | |
| 23 ```{r} | |
| 24 cat('--- View the top 100 rows of the result table ---') | |
| 25 res <- results(dds, contrast = c(opt$X_C, opt$X_T, opt$X_K)) | |
| 26 write.csv(as.data.frame(res), file = opt$X_R) | |
| 27 res_df = as.data.frame(res)[1:100, ] | |
| 28 datatable(res_df, style="bootstrap", filter = 'top', | |
| 29 class="table-condensed", options = list(dom = 'tp', scrollX = TRUE)) | |
| 30 ``` |