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1 ---
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2 output: html_document
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3 ---
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4
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5 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
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6 knitr::opts_chunk$set(
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7 echo = as.logical(opt$X_e),
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8 error = TRUE
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9 )
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10 ```
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11
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12
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13 ```{r eval=TRUE}
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14 # Import workspace
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15 # fcp = file.copy(opt$X_W, "deseq.RData")
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16 load(opt$X_W)
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17 ```
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18
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19 # Results {.tabset}
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20
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21 ## Result table
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22
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23 ```{r}
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24 cat('--- View the top 100 rows of the result table ---')
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25 res <- results(dds, contrast = c(opt$X_C, opt$X_T, opt$X_K))
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26 write.csv(as.data.frame(res), file = opt$X_R)
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27 res_df = as.data.frame(res)[1:100, ]
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28 datatable(res_df, style="bootstrap", filter = 'top',
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29 class="table-condensed", options = list(dom = 'tp', scrollX = TRUE))
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30 ```
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