Mercurial > repos > tomnl > lcms_interval_scheduling

comparison cameradims.R @ 4:fe2d05d5731a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 578fd07833b93847193666c11744ba0bca1aaf57-dirty
author tomnl
date Thu, 03 May 2018 06:59:38 -0400
parents 091367e6e25f
children c48754ef58fa
comparison
equal deleted inserted replaced
3:091367e6e25f 4:fe2d05d5731a
79 79
80 df <- df[df$i>opt$intensity_filter,] 80 df <- df[df$i>opt$intensity_filter,]
81 81
82 82
83 if (opt$rule_type=='extended_large'){ 83 if (opt$rule_type=='extended_large'){
84
85 rule_sep=','
84 opt$rule_type <- 'user' 86 opt$rule_type <- 'user'
85 if(opt$polarity=='pos'){ 87 if(opt$polarity=='pos'){
86 opt$rule_path <- read.csv(system.file("rules", "CAMERA_rules_PosFinal_PlusLi.csv", package = "cameraDIMS"), header=TRUE) 88 opt$rule_path <- system.file("rules", "CAMERA_rules_PosFinal_PlusLi.csv", package = "cameraDIMS")
87 }else{ 89 }else{
88 opt$rule_path <- read.csv(system.file("rules", "CAMERA_rules_NegFinal_PlusLi.csv", package = "cameraDIMS"), header=TRUE) 90 opt$rule_path <- system.file("rules", "CAMERA_rules_NegFinal_PlusLi.csv", package = "cameraDIMS")
89 } 91 }
92 }else{
93 rule_sep='\t'
90 } 94 }
91 95
92 cameraOut <- cameraDIMS(data=df, 96 cameraOut <- cameraDIMS(data=df,
93 params_iso=paramiso, 97 params_iso=paramiso,
94 params_adduct=paramadduct, 98 params_adduct=paramadduct,
95 rule_type=opt$rule_type, 99 rule_type=opt$rule_type,
96 rule_pth=opt$rule_path, 100 rule_pth=opt$rule_path,
97 rule_sep='\t', 101 rule_sep=rule_sep,
98 rule_export=rule_export) 102 rule_export=rule_export)
99 103
100 104
101 print(head(cameraOut[[1]])) 105 print(head(cameraOut[[1]]))
102 print(head(cameraOut[[2]])) 106 print(head(cameraOut[[2]]))