Mercurial > repos > bornea > saint_bubblebeam
comparison bubbles_v9_NSAF_natural_log.R @ 11:80cc85d7d6e3 draft
Uploaded
| author | bornea |
|---|---|
| date | Thu, 19 Nov 2015 13:26:35 -0500 |
| parents | 79285a7acfbf |
| children | 7b797749e8c4 |
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| 10:79285a7acfbf | 11:80cc85d7d6e3 |
|---|---|
| 225 # Check Saintscore cutoff and stop program if not between 0 and 1 | 225 # Check Saintscore cutoff and stop program if not between 0 and 1 |
| 226 ################################################################################################### | 226 ################################################################################################### |
| 227 cutoff_check <- function(cutoff){ | 227 cutoff_check <- function(cutoff){ |
| 228 if( any(cutoff < 0 | cutoff > 1) ) stop('SAINT score cutoff not between 0 and 1. Please correct and try again') | 228 if( any(cutoff < 0 | cutoff > 1) ) stop('SAINT score cutoff not between 0 and 1. Please correct and try again') |
| 229 } | 229 } |
| 230 | |
| 230 ins_check_run <- function() { | 231 ins_check_run <- function() { |
| 231 if ('dplyr' %in% rownames(installed.packages())){} | 232 if ('dplyr' %in% rownames(installed.packages())){} |
| 232 else { | 233 else { |
| 233 install.packages('dplyr', repos='http://cran.us.r-project.org') | 234 install.packages('dplyr', repos='http://cran.us.r-project.org') |
| 234 } | 235 } |
| 240 else { | 241 else { |
| 241 install.packages('ggplot2', repos='http://cran.us.r-project.org') | 242 install.packages('ggplot2', repos='http://cran.us.r-project.org') |
| 242 } | 243 } |
| 243 } | 244 } |
| 244 | 245 |
| 245 ins_check_run() | |
| 246 args <- commandArgs(trailingOnly = TRUE) | 246 args <- commandArgs(trailingOnly = TRUE) |
| 247 main(args[1],args[2],args[3],args[4],args[5],args[6],args[7],args[8],args[9]) | 247 main(args[1],args[2],args[3],args[4],args[5],args[6],args[7],args[8],args[9]) |
| 248 | 248 |
| 249 #main("test_list.txt", "preytest.txt", crapome="craptest.txt", color="crapome", label=TRUE) | 249 #main("test_list.txt", "preytest.txt", crapome="craptest.txt", color="crapome", label=TRUE) |
| 250 #main("Crizo_list.txt", "prey_cr.txt", crapome = "crizo_crap.txt", color="crapome", label=TRUE, cutoff=0.7) | 250 #main("Crizo_list.txt", "prey_cr.txt", crapome = "crizo_crap.txt", color="crapome", label=TRUE, cutoff=0.7) |