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