update docs, fix sarch_spectra bug, change to GPL3

ethanbass · Jan 25, 2023 · 761a213 · 761a213
1 parent e22351a
commit 761a213
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Showing 9 changed files with 620 additions and 33 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -16,7 +16,7 @@ Imports:
     tidyr
 Suggests:
     plotly
-License: MIT + file LICENSE
+License: GPL (>= 3)
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 7.2.1
diff --git a/LICENSE.md b/LICENSE.md
diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,5 @@
 # msdialreadr 0.2.0
 
+* Update license to GPL3.
 * Added a `NEWS.md` file to track changes to the package.
 * Added `search_msp` function to conduct database searches for spectra.
diff --git a/R/attach_metadata.R b/R/attach_metadata.R
@@ -51,3 +51,11 @@ keep_order <- function(data, fn, ...) {
   out[,col] <- NULL
   out
 }
+
+transfer_metadata <- function(new_object, old_object,
+                              exclude = c('names','row.names','class','dim','dimnames')){
+  a <- attributes(old_object)
+  a[exclude] <- NULL
+  attributes(new_object) <- c(attributes(new_object), a)
+  new_object
+}
diff --git a/R/normalization.R b/R/normalization.R
@@ -17,7 +17,8 @@
 #' @author E. Nevedomskaya
 #' @author Rico Derks
 #' @author Ethan Bass
-#' @note Adapted from Rcpm package (https://github.com/ricoderks/Rcpm)
+#' @note Adapted from the \href{https://github.com/ricoderks/Rcpm}{Rcpm} package
+#' by  Rico Derks (licensed under GPL3).
 #' @references Dieterle, F., Ross, A., Schlotterbeck, G. & Senn, H. Probabilistic Quotient
 #' Normalization as Robust Method to Account for Dilution of Complex Biological Mixtures.
 #' Application in H1 NMR Metabonomics. Anal. Chem. 78, 4281-4290 (2006).

diff --git a/R/search_spectra.R b/R/search_spectra.R
@@ -1,4 +1,3 @@
-
 #' Search spectra in MSDIAL alignment against database
 #' @param x An \code{msdial_alignment} object.
 #' @param db MSP database as list
@@ -11,7 +10,7 @@
 #' @param n.results How many results to return.
 #' @param mc.cores How many cores to use for parallel processing? Defaults to 2.
 #' @param ris Retention indices to use
-#' @note See [mspcompiler](https://github.com/QizhiSu/mspcompiler) for help compiling
+#' @note See \href{https://github.com/QizhiSu/mspcompiler}{mspcompiler} for help compiling
 #' an msp database.
 #' @return Returns a modified \code{msdial_alignment} object with database matches
 #' in the \code{matches} slot.
@@ -27,6 +26,9 @@ search_spectra <- function(x, db, cols, ..., ri_thresh = 100, spectral_weight =
   if (missing(ris)){
     ris <- sapply(db, function(x) x$RI)
   }
+  if (missing(cols)){
+    cols <- seq_len(ncol(x$tab))
+  }
   for (col in cols){
     sp <- get_spectrum(x, col)
     ri_diff <- abs(as.numeric(x$peak_meta[col, "Average.RI"]) - ris)
@@ -64,16 +66,16 @@ get_spectrum <- function(x, col){
 #' @param parallel Logical. Whether to use parallel processing. (This feature
 #' does not work on Windows).
 #' @param mc.cores How many cores to use for parallel processing? Defaults to 2.
-#' @param what What kind of object to return. Either \code{msdial_alignment} object (\code{msd})
-#' or \code{data.frame} (\code{df}).
+#' @param what What kind of object to return. Either \code{msdial_alignment} object,
+#'  (\code{msd}), or \code{data.frame} (\code{df}).
 #' @importFrom pbapply pblapply
 #' @importFrom OrgMassSpecR SpectrumSimilarity
 #' @author Ethan Bass
 #' @export
 
 search_msp <- function(x, db, ..., n.results = 10, parallel, mc.cores = 2,
-                       what=c("msd", "df","scores")){
-  # result <- match.arg(result, c("msd", "df", "scores"))
+                       what=c("msd", "df", "scores")){
+  result <- match.arg(result, c("msd", "df", "scores"))
   if (missing(parallel)){
     parallel <- .Platform$OS.type != "windows"
   } else if (parallel & .Platform$OS.type == "windows"){

diff --git a/man/pqn.Rd b/man/pqn.Rd
diff --git a/man/search_msp.Rd b/man/search_msp.Rd
diff --git a/man/search_spectra.Rd b/man/search_spectra.Rd