Mercurial > repos > mingchen0919 > rmarkdown_samtools_flagstat
annotate rmarkdown_samtools_flagstat.Rmd @ 1:a0f0effea707 draft
fix wrong input type error
| author | mingchen0919 |
|---|---|
| date | Wed, 27 Dec 2017 11:55:46 -0500 |
| parents | |
| children | ec39bfeaf496 |
| rev | line source |
|---|---|
| 1 | 1 --- |
| 2 title: 'HTML report title' | |
| 3 output: | |
| 4 html_document: | |
| 5 number_sections: true | |
| 6 toc: true | |
| 7 theme: cosmo | |
| 8 highlight: tango | |
| 9 --- | |
| 10 | |
| 11 ```{r setup, include=FALSE, warning=FALSE, message=FALSE} | |
| 12 knitr::opts_chunk$set( | |
| 13 echo = ECHO, | |
| 14 error = TRUE | |
| 15 ) | |
| 16 ``` | |
| 17 | |
| 18 | |
| 19 # Code for computational analysis | |
| 20 | |
| 21 ```{r 'step 1'} | |
| 22 command = paste0('samtools flagstat ', opt$input_bam, ' > report.csv') | |
| 23 system(command) | |
| 24 read.csv('report.csv') | |
| 25 ``` | |
| 26 | |
| 27 | |
| 28 |