Mercurial > repos > computational-metabolomics > mspurity_createdatabase

comparison purityX.R @ 9:751b7378a683 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/mspurity-galaxy commit 20a48a1862267264f98b7c514287f9a5cba1143f
author computational-metabolomics
date Thu, 13 Jun 2024 11:39:21 +0000
parents efd14b326007
children f5043704dd62
comparison
equal deleted inserted replaced
8:efd14b326007 9:751b7378a683
72 72
73 73
74 74
75 getxcmsSetObject <- function(xobject) { 75 getxcmsSetObject <- function(xobject) {
76 # XCMS 1.x 76 # XCMS 1.x
77 if (class(xobject) == "xcmsSet") { 77 if (class(xobject) == "xcmsSet"){
78 return(xobject) 78 return(xobject)
79 } 79 }
80 # XCMS 3.x 80 # XCMS 3.x
81 if (class(xobject) == "XCMSnExp") { 81 if (class(xobject) == "XCMSnExp") {
82 # Get the legacy xcmsSet object 82 # Get the legacy xcmsSet object
83 suppressWarnings(xset <- as(xobject, "xcmsSet")) 83 suppressWarnings(xset <- as(xobject, "xcmsSet"))
84 sampclass(xset) <- xset@phenoData$sample_group 84 if (!is.null(xset@phenoData$sample_group)){
85 xcms::sampclass(xset) <- xset@phenoData$sample_group
86 }else{
87 xcms::sampclass(xset) <- "."
88 }
85 return(xset) 89 return(xset)
86 } 90 }
87 } 91 }
88 92
89 target_obj <- loadRData(opt$xset_path, opt$rdata_name) 93 target_obj <- loadRData(opt$xset_path, opt$rdata_name)