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comparison rmarkdown_deseq2_count_matrix_render.R @ 1:629323b5fc0c draft

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author mingchen0919
date Sat, 30 Dec 2017 16:39:39 -0500
parents c1f718dd6c7a
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0:c1f718dd6c7a 1:629323b5fc0c
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(DT)
6 library(DESeq2)
5 7
6 ##============ Sink warnings and errors to a file ============== 8 ##============ Sink warnings and errors to a file ==============
7 ## use the sink() function to wrap all code within it. 9 ## use the sink() function to wrap all code within it.
8 ##============================================================== 10 ##==============================================================
9 zz = file('warnings_and_errors.txt') 11 zz = file('warnings_and_errors.txt')
29 # 3. two names in args_list can have common string but one name should not be a part of another name. 31 # 3. two names in args_list can have common string but one name should not be a part of another name.
30 # 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.
31 #+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 33 #+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
32 args_list=list() 34 args_list=list()
33 ##------- 1. input data --------------------- 35 ##------- 1. input data ---------------------
34 args_list$ECHO = c('echo', 'e', '1', 'character') 36 args_list$ECHO = c('echo', 'e', '1', 'logical')
35 args_list$c = c('count_data', 'c', '1', 'character') 37 args_list$c = c('count_data', 'c', '1', 'character')
38 args_list$n = c('count_matrix_column_names', 'n', '1', 'character')
39 args_list$n = c('count_matrix_column_names', 'n', '1', 'character')
36 args_list$C = c('col_data', 'C', '1', 'character') 40 args_list$C = c('col_data', 'C', '1', 'character')
37 args_list$D = c('design_formula', 'D', '1', 'character') 41 args_list$D = c('design_formula', 'D', '1', 'character')
38 args_list$k = c('contrast_condition', 'k', '1', 'character') 42 args_list$k = c('contrast_condition', 'k', '1', 'character')
39 args_list$T = c('treatment', 'T', '1', 'character') 43 args_list$T = c('treatment', 'T', '1', 'character')
40 args_list$K = c('control', 'K', '1', 'character') 44 args_list$K = c('control', 'K', '1', 'character')