Mercurial > repos > mingchen0919 > aurora_htseq
comparison rmarkdown_report.Rmd @ 22:ad2ceb05d152 draft
planemo upload commit 9d80f8019f1eb21b0bc6fdb4e3ae7684174f6ca4-dirty
| author | mingchen0919 |
|---|---|
| date | Fri, 30 Nov 2018 12:02:58 -0500 |
| parents | 69157062629f |
| children |
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| 21:69157062629f | 22:ad2ceb05d152 |
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| 89 | 89 |
| 90 ```{r, echo=TRUE} | 90 ```{r, echo=TRUE} |
| 91 count_data = read.table(paste0(opt$X_d, '/counts.txt'), row.names = 1) | 91 count_data = read.table(paste0(opt$X_d, '/counts.txt'), row.names = 1) |
| 92 sample_names = trimws(strsplit(opt$X_B, ',')[[1]]) | 92 sample_names = trimws(strsplit(opt$X_B, ',')[[1]]) |
| 93 colnames(count_data) = rep(sample_names, length = ncol(count_data)) | 93 colnames(count_data) = rep(sample_names, length = ncol(count_data)) |
| 94 # kable(head(count_data)) | 94 |
| 95 | 95 |
| 96 # modify column names | 96 # modify column names |
| 97 count_data = data.frame(feature_id = rownames(count_data), count_data) | 97 count_data = data.frame(feature_id = rownames(count_data), count_data) |
| 98 write.csv(count_data, | 98 write.csv(count_data, |
| 99 file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/count_data.csv'), | 99 file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/count_data.csv'), |