Module: humsf09 Description: Human SLiMFinder '09 Analysis Module Version: 0.5 Last Edit: 13/07/10

Copyright © 2010 Richard J. Edwards - See source code for GNU License Notice

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Imported modules: comparimotif_V3 rje rje_db rje_zen slimfrap rje_slim rje_dismatrix_V2

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

Function

Custom module for revised Human SLiMFinder (May '09 data) analysis module.

INPUT OPTIONS

resfiles=LIST : List of results files to read in and process []
resdir=PATH : Path to extra SLiMFinder results files (*.occ.csv) []
pairwise=FILE : Pingu Pairwise PPI file [None]
elm=FILE : File of ELM Motifs [None]
nandr=FILE : File of Neduva & Russell motifs [None]
pickledata=FILE : Genemap pickle to import and use. (See other rje_genemap options) [None]
domtable=FILE : Table of domain predictions [None]
direct=LIST : Evidence codes for direct interactions []
indirect=LIST : Evidence codes for indirect interactions []
usego=T/F : Whether to use GO datasets [False]
usenandr=T/F : Whether to use Neduva & Russell results [False]

PROCESSING OPTIONS

badcloud=LIST : List of clouds to screen out (errors) generics=LIST : List of pattern annotation to screen as generic motifs []
knowns=FILE : File containing known SLiMs with columns "Pattern" & "Known" tp=FILE : File containing known SLiMs with columns "Known", "Hub" & "Type" annotate=T/F : Whether to manually annotate/classify SLiMs [False]
skipknown=T/F : Whether to skip known SLiMs in manual annotation (True), or ask to check (False) [False]
skipann=LIST : List of auto-annotations to skip from manual annotation [rand] screenelm=LIST : List of ELMs to screen from CompariMotif [LIG_Sin3_3,TRG_NES_1]
fdranncut=X : FDR cut-off for manual annotation [0.05]
slimjim=T/F : Whether to process data for SLiMJIM output [True]
seqwt=T/F : Perform SeqWt FDR calculations [True]

OUTPUT OPTIONS

frapout=T/F : Whether to generate SLiMFRAP 0.0 output tables [False]

See also rje.py generic commandline options.

History Module Version History

    # 0.0 - Initial Compilation.
    # 0.1 - IRIDIS file clean up & organise method.
    # 0.2 - Added SeqWeight and Connectivity
    # 0.3 - Added new SeqWeight.
    # 0.4 - Improved annotation.
    # 0.5 - Added output for Pingu/GO analysis.