Version for reactomics paper

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 automately generate parameter based on data
• update with citation of cc paper

pmd 0.1.9

• CRAN

pmd 0.1.8

• update kegg/hmdb database
• update getsda to use largest average distance to find pmd freqency 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 furthor reduce the GlobalStd peaks
• remove hmdbp data since pmd network analysis could cover this topic
• remove the dependance of group for quantitative paired peaks
• improve shiny application for sda analysis

CRAN version

• 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
• 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 correlationship in getpmd
• add support for quantitative paired peaks list selection for specific reaction
• add support for target pmd and compound analysis for reaction chain
• update vignettes
• change default ng value into auto-detection
• add top option to limit sda output
• add suport for GlobalStd based targeted analysis
• add suport 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

CRAN version

This version is the stable version on CRAN. Results should be the same as published paper.