Changelog

Source: NEWS.md

pmd 0.2.6

  • Add getpmddf to show pmd details with given m/z only data and m/z group information(optional, segmentation m/z group for spatial reactomics analysis)
  • Update reactomics vignette with section “Reactomics analysis for MS only data” and showcase the quantitative analysis for certain PMD
  • add support for mass only data for getchain

pmd 0.2.5

  • Add KEGG reaction class and enzyme number to the keggrall database
  • Fix url of demo data

pmd 0.2.4

  • add support for mass only data for quantitative reactomics analysis
  • add quantitative methods for dynamic pmds
  • add support for multiple pmds in getpmd function
  • update reactomics vignette to add more details for quantitative analysis of PMD
  • update getchain to handle large data
  • add mass defect filter for getrda and getpaired to retain reaction related PMDs
  • add parameter for getrda for pmd sets and mass defect table
  • change getchain corcutoff to 0.6

pmd 0.2.3

  • add MaConDa database
  • fix NULL default value issue in shiny apps

pmd 0.2.2

  • spell check
  • goodpractice package check

pmd 0.2.12021-01-21

  • CRAN

pmd 0.2.0

  • add option to skip sda in GlobalStd algorithm and set default to F
  • organize the R files
  • add vignette for reactomics analysis
  • add correlation directed analysis function
  • modified getcorcluster function to find independent peaks
  • add vignette section for reduced independent peaks selection in GlobalStd algorithm
  • fix the issue for getchain with multiple masses
  • fix the correlation issue in pos/neg linkage function
  • Output within RT clusters high frequencies PMD(s) as message for user to check
  • Change default ng to NULL in getpared function for automated generate parameter based on data
  • update with citation of cc paper
  • fix the bug in pmd ms/ms annotation due to the change of enviGCMS package
  • fix the order issue from CRAN

pmd 0.1.92020-06-04

  • CRAN

pmd 0.1.8

  • update kegg/hmdb database
  • update getsda to use largest average distance to find pmd frequency cutoff, more robust to large dataset

pmd 0.1.7

  • add function for pmd ms/ms annotation
  • add function to read in msp file as database
  • detach rcdk package
  • add function to link pos/neg by pmd

pmd 0.1.6

  • rewrite getchain to speed up
  • add shiny application pmdnet to perform PMD network analysis
  • add support for formula in getchain to find compounds ions
  • remove frequency cutoff in getsda and use PMD network clusters analysis to determine the cutoff
  • add merge feature for getcluster and such methods could be used to further reduce the GlobalStd peaks
  • remove hmdbp data since pmd network analysis could cover this topic
  • remove the dependence of group for quantitative paired peaks
  • improve shiny application for sda analysis

pmd 0.1.52019-08-22

  • CRAN

pmd 0.1.4

  • isotope selection improved to get rid of 1&2 issue
  • fix top issue in getsda
  • fix peak index issue in getcluster
  • add corcutoff for getpmd

pmd 0.1.3

  • speed up GlobalStd by mapply
  • add message for getrda
  • add hmdb pmd analysis results as dataset
  • add digits for mass accuracy
  • fix the ms1 larger issue in getpmd
  • add correlations in getpmd
  • add support for quantitative paired peaks list selection for specific reaction
  • add support for target pmd and compound analysis for reaction chain

pmd 0.1.2

  • update vignettes
  • change default ng value into auto-detection
  • add top option to limit sda output
  • add support for GlobalStd based targeted analysis
  • add support to extract specific pmd across different retention time groups
  • add PCA similarity factor function from EvolQG package
  • add support to export std peaks based on correlation within retention time group
  • add support to export index for peaks with highest intensity in peaks cluster
  • add support to use intensity data to refine GlobalStd results
  • add support to generate sda analysis for mass list only #5
  • remove multi chargers with a strict rule #4
  • add parameter selection part in vignette #3
  • add support for peaks cluster output #2
  • add support for formula generation in enviGCMS package #1

pmd 0.1.12018-12-02

pmd 0.1.0

  • new package for paired mass distance analysis