diff --git a/DESCRIPTION b/DESCRIPTION index 50e915e4712a96296a47104a6e587d3f89a293e0..895284ae7ed03213468b5a6b2e4a66ffbf5c6031 100755 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: RMassBank Type: Package Title: Workflow to process tandem MS files and build MassBank records -Version: 2.3.1 +Version: 2.7.0 Authors@R: c( person(given = "RMassBank at Eawag", email = "massbank@eawag.ch", role=c("cre")), diff --git a/R/getSplash.R b/R/getSplash.R index 409745c93dbd5f2403aa131aacb571873ec98cad..8dfd8ca11144a66a0802f60c4dbafd2d5a7ca353 100644 --- a/R/getSplash.R +++ b/R/getSplash.R @@ -62,8 +62,8 @@ filter_spectrum <- function(peaks, top_ions = NULL, base_peak_percentage = NULL) peaks <- peaks[peaks[,2] >= base_peak_percentage * base_peak_intensity, , drop=FALSE] } - ## Filter by top ions if specified - if (!missing(top_ions)) { + return(splash) +} o <- order(-1*peaks[,2], peaks[,1], decreasing=FALSE)[seq(1:min(top_ions, nrow(peaks)))] peaks <- peaks[o, , drop=FALSE] } diff --git a/R/leMsmsRaw.R b/R/leMsmsRaw.R index 72c44b4189a925d701e38752fc496b62c675f29c..ea27235a484da216d99bcc85b8a54923f7439760 100644 --- a/R/leMsmsRaw.R +++ b/R/leMsmsRaw.R @@ -245,6 +245,14 @@ findMsMsHR.mass <- function(msRaw, mz, limit.coarse, limit.fine, rtLimits = NA, childHeaders <- headerData[(headerData$precursorScanNum == masterScan) & (headerData$precursorMZ > mz - limit.coarse) & (headerData$precursorMZ < mz + limit.coarse) ,] + + # Fix 9.10.17: headers now include non-numeric columns, leading to errors in data conversion. + # Remove non-numeric columns + headerCols <- colnames(masterHeader) + headerCols <- headerCols[unlist(lapply(headerCols, function(col) is.numeric(masterHeader[,col])))] + masterHeader <- masterHeader[,headerCols,drop=FALSE] + childHeaders <- childHeaders[,headerCols,drop=FALSE] + childScans <- childHeaders$seqNum msPeaks <- mzR::peaks(msRaw, masterHeader$seqNum)