Mercurial > repos > computational-metabolomics > mspurity_createdatabase
comparison flagRemove.R @ 9:751b7378a683 draft
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20a48a1862267264f98b7c514287f9a5cba1143f
author | computational-metabolomics |
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date | Thu, 13 Jun 2024 11:39:21 +0000 |
parents | efd14b326007 |
children |
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8:efd14b326007 | 9:751b7378a683 |
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1 library(msPurity) | 1 library(msPurity) |
2 library(xcms) | |
2 library(optparse) | 3 library(optparse) |
3 print(sessionInfo()) | 4 print(sessionInfo()) |
4 option_list <- list( | 5 option_list <- list( |
5 make_option(c("-o", "--out_dir"), | 6 make_option(c("-o", "--out_dir"), |
6 type = "character", default = getwd(), | 7 type = "character", default = getwd(), |
115 } | 116 } |
116 | 117 |
117 | 118 |
118 print(opt) | 119 print(opt) |
119 | 120 |
120 getxcmsSetObject <- function(xobject) { | 121 # This R function can handle both XCMS object versions (so following code |
121 # XCMS 1.x | 122 # no longer required - kept here for reference) |
122 if (class(xobject) == "xcmsSet") { | 123 # getxcmsSetObject <- function(xobject) { |
123 return(xobject) | 124 # # XCMS 1.x |
124 } | 125 # if (class(xobject) == "xcmsSet"){ |
125 # XCMS 3.x | 126 # return(xobject) |
126 if (class(xobject) == "XCMSnExp") { | 127 # } |
127 # Get the legacy xcmsSet object | 128 # # XCMS 3.x |
128 suppressWarnings(xset <- as(xobject, "xcmsSet")) | 129 # if (class(xobject) == "XCMSnExp") { |
129 xcms::sampclass(xset) <- xset@phenoData$sample_group | 130 # # Get the legacy xcmsSet object |
130 return(xset) | 131 # suppressWarnings(xset <- as(xobject, "xcmsSet")) |
131 } | 132 # if (!is.null(xset@phenoData$sample_group)){ |
132 } | 133 # xcms::sampclass(xset) <- xset@phenoData$sample_group |
134 # }else{ | |
135 # xcms::sampclass(xset) <- "." | |
136 # } | |
137 # return(xset) | |
138 # } | |
139 # } | |
133 | 140 |
134 | 141 |
135 loadRData <- function(rdata_path, name) { | 142 loadRData <- function(rdata_path, name) { |
136 # loads an RData file, and returns the named xset object if it is there | 143 # loads an RData file, and returns the named xset object if it is there |
137 load(rdata_path) | 144 load(rdata_path) |
138 return(get(ls()[ls() %in% name])) | 145 return(get(ls()[ls() %in% name])) |
139 } | 146 } |
140 | 147 |
141 xset <- getxcmsSetObject(loadRData(opt$xset_path, c("xset", "xdata"))) | 148 xset <- loadRData(opt$xset_path, c("xset", "xdata")) |
142 | 149 |
143 print(xset) | 150 |
144 if (is.null(opt$samplelist)) { | 151 if (is.null(opt$samplelist)) { |
145 blank_class <- opt$blank_class | 152 blank_class <- opt$blank_class |
146 } else { | 153 } else { |
147 samplelist <- read.table(opt$samplelist, sep = "\t", header = TRUE) | 154 samplelist <- read.table(opt$samplelist, sep = "\t", header = TRUE) |
148 samplelist_blank <- unique(samplelist$sample_class[samplelist$blank == "yes"]) | 155 samplelist_blank <- unique(samplelist$sample_class[samplelist$blank == "yes"]) |
153 quit() | 160 quit() |
154 } | 161 } |
155 blank_class <- as.character(chosen_blank) | 162 blank_class <- as.character(chosen_blank) |
156 print(blank_class) | 163 print(blank_class) |
157 } | 164 } |
165 | |
166 | |
158 | 167 |
159 | 168 |
160 if (is.null(opt$multilist)) { | 169 if (is.null(opt$multilist)) { |
161 ffrm_out <- flag_remove(xset, | 170 ffrm_out <- flag_remove(xset, |
162 pol = opt$polarity, | 171 pol = opt$polarity, |
199 file.path(opt$out_dir, "removed_peaks.tsv"), | 208 file.path(opt$out_dir, "removed_peaks.tsv"), |
200 row.names = FALSE, sep = "\t" | 209 row.names = FALSE, sep = "\t" |
201 ) | 210 ) |
202 } else { | 211 } else { |
203 # nolint start | 212 # nolint start |
204 # TODO | 213 # TODO - potential for multilist analysis (e) |
205 # xsets <- split(xset, multilist_df$multlist) | |
206 # | |
207 # mult_grps <- unique(multilist_df$multlist) | |
208 # | |
209 # for (mgrp in mult_grps){ | |
210 # xset_i <- xsets[mgrp] | |
211 # xcms::group(xset_i, | |
212 # | |
213 # } | |
214 # nolint end | 214 # nolint end |
215 } | 215 } |