remove pmdanno function to rmwf package

DESCRIPTION

@@ -14,8 +14,7 @@ Encoding: UTF-8
 LazyData: true
 Suggests: knitr,
     shiny,
-    rmarkdown,
-    MSnbase
+    rmarkdown
 VignetteBuilder: knitr
 biocViews: 
 Depends: R (>= 3.5.0)
@@ -26,4 +25,4 @@ Imports: RColorBrewer,
         data.table,
         igraph,
         enviGCMS
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2

NAMESPACE

@@ -24,6 +24,5 @@ export(plotsda)
 export(plotstd)
 export(plotstdrt)
 export(plotstdsda)
-export(pmdanno)
 export(runPMD)
 export(runPMDnet)

NEWS.md

@@ -2,6 +2,7 @@
 
 - CRAN
 - Change URL to doi for citation
+- remove dependance of msnbase
 
 # pmd 0.2.6
 

R/pmdanno.R

@@ -166,80 +166,3 @@ getmspmd <- function(file, digits = 2, icf = 10) {
                 msmsraw = unname(msmsraw)
         ))
 }
-
-#' Perform MS/MS pmd annotation for mgf file
-#' @param file mgf file generated from MS/MS data
-#' @param db database could be list object from `getms2pmd`
-#' @param ppm mass accuracy, default 10
-#' @param prems precursor mass range, default 1.1 to include M+H or M-H
-#' @param pmdc pmd length percentage cutoff for annotation. 0.6(default) means 60 percentage of the pmds in your sample could be found in certain compound pmd database
-#' @param scutoff relative intensity cutoff for input spectra for pmd analysis, default 0.1
-#' @return list with MSMS annotation results
-#' @export
-pmdanno <- function(file,
-                    db = NULL,
-                    ppm = 10,
-                    prems = 1.1,
-                    pmdc = 0.6,
-                    scutoff = 0.1) {
-        namemgf <- basename(file)
-        sample <- MSnbase::readMgfData(file)
-        prec <- MSnbase::precursorMz(sample)
-        mz <- MSnbase::mz(sample)
-        ins <- MSnbase::intensity(sample)
-        idx <- unlist(ins) / max(unlist(ins)) > scutoff
-        if (sum(idx) > 0) {
-                mz <- unlist(mz)[idx]
-                ins <- unlist(ins)[idx]
-                ins <- ins / max(ins) * 100
-                pmdt <- stats::dist(mz, method = "manhattan")
-
-                if (is.list(db)) {
-                        pmdt <-
-                                unique(round(as.numeric(pmdt), digits = 2))
-                        range <- cbind(db$mz - prems, db$mz + prems)
-                        mza <- data.table::as.data.table(cbind.data.frame(mzmin=db$mz - prems,mzmax= db$mz + prems))
-                        mzb <- data.table::as.data.table(cbind.data.frame(mzmin=prec - ppm / prec*1e-06,mzmax= prec + ppm / prec*1e-06))
-                        colnames(mza) <- colnames(mzb) <- c("min","max")
-                        data.table::setkey(mzb, min, max)
-                        overlapms <- data.table::foverlaps(mza, mzb, which = TRUE)
-                        over <- overlapms[stats::complete.cases(overlapms)&!duplicated(overlapms),]
-                        re <- data.frame(over)
-                        if (nrow(re) > 0) {
-                                msmsd <- db$msms[re$xid]
-                                name <- db$name[re$xid]
-                                mz2 <- db$mz[re$xid]
-                                msmsraw <- db$msmsraw[re$xid]
-
-                                result <- vapply(msmsd, function(x)
-                                        sum(pmdt %in% unique(x)),1)
-                                result <- c(result)
-
-                                if (sum(result > length(pmdt) * pmdc) == 0) {
-                                        return(NULL)
-                                } else{
-                                        re0 <- result[result > length(pmdt) * pmdc]
-                                        order <- order(re0,decreasing = TRUE)
-                                        t <-
-                                                list(
-                                                        name = name[result > length(pmdt) * pmdc][order],
-                                                        mz = mz2[result > length(pmdt) * pmdc][order],
-                                                        msms = msmsd[result > length(pmdt) * pmdc][order],
-                                                        msmsraw = msmsraw[result > length(pmdt) * pmdc][order],
-                                                        dmz = mz,
-                                                        dprc = prec,
-                                                        dins = ins,
-                                                        file = namemgf
-                                                )
-                                        return(t)
-                                }
-                        } else{
-                                return(NULL)
-                        }
-                } else{
-                        return(NULL)
-                }
-        } else{
-                return(NULL)
-        }
-}