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Automated Processing of High-resolution Intensity Data

Program: APHID
Description: Automated Processing of High-resolution Intensity Data
Version: 2.2
Last Edit: 10/07/14
Citation: Raab et al. (2010), Proteomics 10: 2790-2800.

Copyright © 2007 Richard J. Edwards - See source code for GNU License Notice

Imported modules: rje rje_db rje_genemap rje_scoring rje_seq rje_slimcore gablam pingu_V3 rje_dismatrix_V2

See SLiMSuite Blog for further documentation. See rje for general commands.


APHID takes for input the partially processed results of MS analysis, with intensity data, filters based on scores thresholds, removes redundancy (using PINGU) and calculates relative intensity scores. PINGU is then used to generate outputs for use with Cytoscape and other visualisation tools.

Input takes the form of a delimited text file with the following column headers: Expt, Subpop, Identifier, logInt, Score. In addition, other columns may be present (and may be used to filter data). The "unique" column headers allow individual identifications to be isolated, which is important for data filtering and intensity mapping.

Intensities are converted into relative intensities with two options: (1) the redundancy level determines which results are combined. This may be simply at the identified peptide level, the gene level, or even at the protein family level (as determined through BLAST homology). If "fam" is used then GABLAM will be used to generate families for a given level of identity.

Note. Core functionality has not been checked/developed since 2010.


Input Options

data=FILE : Delimited file containing input data [None]
seqin=FILE : Sequence file containing hits (if pepnorm != count) [None]
basefile=X : Text base for output files and resdir [default based on data file name]
unique=LIST : Headers that, with Identifier, Treatment & Replicate, constitute unique entries [Slice]
identifier=X : Column containing protein indentifications [Identifier]
treatment=X : Column heading to identify different experimental treatment samples (e.g. condition/control) [Treatment]
replicate=X : Column heading to identify experimntal replicates [Replicate]
intensity=X : Column containing intensity values [logInt]
logint=T/F : Whether intensity value is a log intensity [True]
pepcount=X : Column containing peptide counts [rI]
statfilter=LIST : List of filters for data [Score>-3]
force=T/F : Regenerate intermediate files even if found [False]

Intensity Combination Options

nr=X : Level for redundancy removal (gene/pep/fam) [gene]
famcut=X : Percentage identity to be used by GABLAM for clustering [0.0]
normalise=X : Scoring strategy for normalising intensity (ppm/shared/none/mwt/frag/count) [ppm]
flatout=T/F : Whether to output reduced GeneMap flatfiles (*.data.tdt & *.aliases.tdt) [False]

Enrichment options

absence=X : Min normalised combined score (arbitrarily assigned to proteins totally absent from samples) [0.5]
combine=X : Methods for combining different replicates (max,mean,min,geo,full) [mean]
convert=LIST : List of X:Y where Treatment X will be renamed Y []
enrpairs=LIST : List of X:Y where enrichment will be restricted to X:Y ratios []
jackknife=T/F : Whether to perform jack-knifing tests on enrpairs [True]
enrcut=X : Enrichment > X for jack-knifing test [1.0]
blanks=T/F : Whether to include most blank enrichment/jacknife rows for missing NRID [True]

History Module Version History

    # 0.0 - Initial Compilation.
    # 0.1 - Added fam NR using GABLAM and SLiMCore.
    # 0.2 - Added replicates and pepnum abundance.
    # 0.3 - Improvements incorporating GeneMap version of Pingu.
    # 0.4 - Allowed mutliple runs from one call. Added fullmonty option. Moved and corrected compare mode.
    # 1.0 - Full initial working version.
    # 1.1 - Added PNG visualisations.
    # 1.2 - Added additional filtering according to replicate counts (minrep=X).
    # 1.3 - Added additional filtering according to min peptide occurrences (minpep=X,Y)
    # 2.0 - Reduced options and tidied code substantially with additional intermediate data outputs.
    # 2.1 - Reduced import commands.
    # 2.2 - Updated for revised SLiMCore.
    # 2.2.1 - Minor bug fix.

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