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comparison rmarkdown_feature_counts_render.R @ 11:238d57ce7d74 draft

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update
author mingchen0919
date Fri, 29 Dec 2017 14:07:35 -0500
parents 1cff3a3e2b94
children 7a2369ab4f84
comparison
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10:1cff3a3e2b94 11:238d57ce7d74
1 library(getopt) 1 library(getopt)
2 library(rmarkdown) 2 library(rmarkdown)
3 library(htmltools) 3 library(htmltools)
4 library(dplyr) 4 library(dplyr)
5 library(Rsubread) 5 library(Rsubread)
6 library(DT)
6 7
7 ##============ Sink warnings and errors to a file ============== 8 ##============ Sink warnings and errors to a file ==============
8 ## use the sink() function to wrap all code within it. 9 ## use the sink() function to wrap all code within it.
9 ##============================================================== 10 ##==============================================================
10 zz = file('warnings_and_errors.txt') 11 zz = file('warnings_and_errors.txt')
31 # for example, one name is "ECHO", if another name is "ECHO_XXX", it will cause problems. 32 # for example, one name is "ECHO", if another name is "ECHO_XXX", it will cause problems.
32 #+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 33 #+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
33 args_list=list() 34 args_list=list()
34 ##------- 1. input data --------------------- 35 ##------- 1. input data ---------------------
35 args_list$e = c('echo', 'e', '1', 'logical') 36 args_list$e = c('echo', 'e', '1', 'logical')
36 args_list$a = c('input_bam', 'a', '1', 'character') 37 args_list$a = c('input_bam_paths', 'a', '1', 'character')
38 args_list$N = c('input_bam_names', 'N', '1', 'character')
37 args_list$b = c('annot_inbuilt', 'b', '1', 'character') 39 args_list$b = c('annot_inbuilt', 'b', '1', 'character')
38 args_list$c = c('annot_ext', 'c', '1', 'character') 40 args_list$c = c('annot_ext', 'c', '1', 'character')
39 args_list$f = c('isGTFAnnotationFile', 'f', '1', 'logical') 41 args_list$f = c('isGTFAnnotationFile', 'f', '1', 'logical')
40 args_list$g = c('gtf_feature_type', 'g', '1', 'character') 42 args_list$g = c('gtf_feature_type', 'g', '1', 'character')
41 args_list$h = c('gtf_attr_type', 'h', '1', 'character') 43 args_list$h = c('gtf_attr_type', 'h', '1', 'character')