Mercurial > repos > tomnl > create_msp

comparison anticipated_purity_dims.R @ 2:ac8738f96e53 draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
author tomnl
date Wed, 02 May 2018 14:25:04 -0400
parents 3f1f2d545f3a
children 3ecba7815437
comparison
equal deleted inserted replaced
1:3f1f2d545f3a 2:ac8738f96e53
40 indf$i <- indf[,colnames(indf)==filename] 40 indf$i <- indf[,colnames(indf)==filename]
41 indf[,colnames(indf)==filename] <- as.numeric(indf[,colnames(indf)==filename]) 41 indf[,colnames(indf)==filename] <- as.numeric(indf[,colnames(indf)==filename])
42 42
43 filename = sub("raw", "mzML", filename, ignore.case = TRUE) 43 filename = sub("raw", "mzML", filename, ignore.case = TRUE)
44 print(filename) 44 print(filename)
45 df <- indf[4:nrow(indf),] 45 df <- indf[3:nrow(indf),]
46 if ('blank_flag' %in% colnames(df)){ 46 if ('blank_flag' %in% colnames(df)){
47 df <- df[df$blank_flag==1,] 47 df <- df[df$blank_flag==1,]
48 } 48 }
49 49
50 colnames(df)[colnames(df)=='m.z'] <- 'mz' 50 colnames(df)[colnames(df)=='m.z'] <- 'mz'
51 51
52 if ('nan' %in% df$mz){ 52 if ('nan' %in% df$mz){
53 df[df$mz=='nan',]$mz <- NA 53 df[df$mz=='nan',]$mz <- NA
54 } 54 }
55 df$mz <- as.numeric(df$mz) 55 df$mz <- as.numeric(df$mz)
56 56 mzml_file <- file.path(opt$mzML_file, filename)
57 57
58 58
59 59
60 } 60 }
61 61
75 }else{ 75 }else{
76 isotopes <- TRUE 76 isotopes <- TRUE
77 } 77 }
78 78
79 79
80 if (dir.exists(opt$mzML_file)){
81 # if directory then we need to add a file name
82 print(filename)
83 if (is.na(filename)){
84 print('ERROR: If a directory is provided then a filename needs to be entered
85 directory or automatically obtained by using a dimspy output')
86 quit()
87 }else{
88 mzml_file <- file.path(opt$mzML_file, filename)
89 }
90 }else{
91 mzml_file <- opt$mzML_file
92 }
93 80
94 if (is.null(opt$sim)){ 81 if (is.null(opt$sim)){
95 sim=FALSE 82 sim=FALSE
96 }else{ 83 }else{
97 sim=TRUE 84 sim=TRUE
116 iwNormFun = msPurity::iwNormQE.5() 103 iwNormFun = msPurity::iwNormQE.5()
117 } 104 }
118 105
119 print('FIRST ROWS OF PEAK FILE') 106 print('FIRST ROWS OF PEAK FILE')
120 print(head(df)) 107 print(head(df))
121 108 print(mzml_file)
122 predicted <- msPurity::dimsPredictPuritySingle(df$mz, 109 predicted <- msPurity::dimsPredictPuritySingle(df$mz,
123 filepth=mzml_file, 110 filepth=mzml_file,
124 minOffset=minOffset, 111 minOffset=minOffset,
125 maxOffset=maxOffset, 112 maxOffset=maxOffset,
126 ppm=opt$ppm, 113 ppm=opt$ppm,