Mercurial > repos > bornea > saint_preproc

comparison pre_process_protein_name_set.R @ 20:e21be0412789 draft

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author bornea
date Thu, 19 Nov 2015 13:31:59 -0500
parents c56ebf254e89
children 9e0a894d2676
comparison
equal deleted inserted replaced
19:c56ebf254e89 20:e21be0412789
1 ins_check_run <- function() {
2 if ("affy" %in% rownames(installed.packages())){}
3 else {
4 source("https://bioconductor.org/biocLite.R")
5 biocLite(c('mygene','affy'))
6 }
7 if ('data.table' %in% rownames(installed.packages())){}
8 else {
9 install.packages('data.table', repos='http://cran.us.r-project.org')
10 }
11 if ('stringr' %in% rownames(installed.packages())){}
12 else {
13 install.packages('stringr', repos='http://cran.us.r-project.org')
14 }
15 if ('VennDiagram' %in% rownames(installed.packages())){}
16 else {
17 install.packages('VennDiagram', repos='http://cran.us.r-project.org')
18 }
19 }
20
1 ins_check_run() 21 ins_check_run()
2 library(data.table) 22 library(data.table)
3 library(affy) 23 library(affy)
4 library(stringr) 24 library(stringr)
5 library(mygene) 25 library(mygene)
71 Tukeys_df[i,j] = 2^(tukey.biweight(mapped_peptides_unique_subset[,j])) 91 Tukeys_df[i,j] = 2^(tukey.biweight(mapped_peptides_unique_subset[,j]))
72 } 92 }
73 } 93 }
74 return(Tukeys_df) 94 return(Tukeys_df)
75 } 95 }
76 ins_check_run <- function() {
77 if ("affy" %in% rownames(installed.packages())){}
78 else {
79 source("https://bioconductor.org/biocLite.R")
80 biocLite(c('mygene','affy'))
81 }
82 if ('data.table' %in% rownames(installed.packages())){}
83 else {
84 install.packages('data.table', repos='http://cran.us.r-project.org')
85 }
86 if ('stringr' %in% rownames(installed.packages())){}
87 else {
88 install.packages('stringr', repos='http://cran.us.r-project.org')
89 }
90 if ('VennDiagram' %in% rownames(installed.packages())){}
91 else {
92 install.packages('VennDiagram', repos='http://cran.us.r-project.org')
93 }
94 }
95 96
96 args <- commandArgs(trailingOnly = TRUE) 97 args <- commandArgs(trailingOnly = TRUE)
97 main(args[1]) 98 main(args[1])