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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 # `DESeqDataSet` object
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13
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14 ```{r 'DESeqDataSet object'}
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15 count_file_paths = strsplit(opt$X_P, ',')[[1]]
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16 count_file_names = strsplit(opt$X_N, ',')[[1]]
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17 sample_table = read.table(opt$X_S, header = TRUE)
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18 row.names(sample_table) = sample_table[,2]
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19 sample_table = sample_table[count_file_names, ]
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20
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21 ## copy count files into OUTPUT_DIR/counts
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22 dir.create(paste0(OUTPUT_DIR, '/counts'), recursive = TRUE)
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23 file_copy = file.copy(count_file_paths, paste0(OUTPUT_DIR, '/counts/', count_file_names), overwrite = TRUE)
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24
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25 ## DESeqDataSet object
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26 dds = DESeqDataSetFromHTSeqCount(sampleTable = sample_table,
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27 directory = paste0(OUTPUT_DIR, '/counts'),
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28 design = formula(opt$X_p))
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29 dds
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30 ```
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