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author mingchen0919
date Sat, 01 Dec 2018 01:27:08 -0500
parents 467a1895c718
children
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1 ---
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2 title: 'HTSeq-count Analysis'
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3 output:
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4 html_document:
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5 highlight: pygments
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6 ---
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8 ## Job script
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10 ```{bash, echo=FALSE}
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11 sh ${TOOL_INSTALL_DIR}/build-and-run-job-scripts.sh > ${REPORT_FILES_PATH}/log.txt 2>&1
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12 ```
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14 ```{r echo=FALSE, comment='', results='asis'}
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15 cat('```bash\n')
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16 cat(readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/htseq-count.sh')), sep = '\n')
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17 cat('\n```')
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18 ```
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20 ## Counts
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22 Write data into a CSV file.
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24 ```{r, echo=TRUE}
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25 count_data = read.table(paste0(opt$X_d, '/counts.txt'), row.names = 1)
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26 sample_names = trimws(strsplit(opt$X_B, ',')[[1]])
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27 colnames(count_data) = rep(sample_names, length = ncol(count_data))
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30 # modify column names
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31 count_data = data.frame(feature_id = rownames(count_data), count_data)
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32 write.csv(count_data,
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33 file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/count_data.csv'),
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34 quote = FALSE, row.names = FALSE)
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35 ```
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37 Display the top 1000 rows with largest average counts.
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39 ```{r echo=TRUE}
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40 # Sort count table by count average
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41 rownames(count_data) = count_data$feature_id
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42 count_data = count_data[, -1]
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43 sorted_ct_table = count_data[order(rowMeans(count_data), decreasing = TRUE), ]
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44 DT::datatable(head(sorted_ct_table, 1000))
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45 ```
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