Mercurial > repos > tomnl > deconrank
comparison cameradims.R @ 4:b37f97bda760 draft
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit d4159f1962ef3fe37dd4f3047e4050afe013c15a-dirty
| author | tomnl |
|---|---|
| date | Thu, 03 May 2018 05:20:17 -0400 |
| parents | defa57c7775e |
| children | e91c400c6ca6 |
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| 3:11ee7db33f60 | 4:b37f97bda760 |
|---|---|
| 77 | 77 |
| 78 df$i <- as.numeric(df$i) | 78 df$i <- as.numeric(df$i) |
| 79 | 79 |
| 80 df <- df[df$i>opt$intensity_filter,] | 80 df <- df[df$i>opt$intensity_filter,] |
| 81 | 81 |
| 82 | |
| 83 if (opt$rule_type=='extended_large'){ | |
| 84 if(opt$polarity=='pos'){ | |
| 85 opt$rule_path <- read.csv(system.file("rules", "CAMERA_rules_PosFinal_PlusLi.csv", package = "cameraDIMS"), header=TRUE) | |
| 86 }else{ | |
| 87 opt$rule_path <- read.csv(system.file("rules", "CAMERA_rules_NegFinal_PlusLi.csv", package = "cameraDIMS"), header=TRUE) | |
| 88 } | |
| 89 } | |
| 90 | |
| 82 cameraOut <- cameraDIMS(data=df, | 91 cameraOut <- cameraDIMS(data=df, |
| 83 params_iso=paramiso, | 92 params_iso=paramiso, |
| 84 params_adduct=paramadduct, | 93 params_adduct=paramadduct, |
| 85 rule_type=opt$rule_type, | 94 rule_type=opt$rule_type, |
| 86 rule_pth=opt$rule_path, | 95 rule_pth=opt$rule_path, |