METAL Command Reference
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Revision as of 07:36, 25 March 2011 by Goncalo (talk | contribs) (→Genomic Control Correction of Input Statistics)
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Describing Input Files
SEPARATOR [WHITESPACE|COMMA|BOTH|TAB] (default = WHITESPACE) COLUMNCOUNTING [STRICT|LENIENT] (default = 'STRICT') MARKERLABEL [LABEL] (default = 'MARKER') ALLELELABELS [LABEL1 LABEL2] (default = 'ALLELE1','ALLELE2') EFFECTLABEL [LABEL|log(LABEL)] (default = 'EFFECT') FLIP
Additional details on the COLUMNCOUNTING and EFFECTLABEL options are available.
Filtering Input Files
ADDFILTER [LABEL CONDITION VALUE] (example = ADDFILTER N > 10) (available conditions are <, >, <=, >=, =, !=, IN) REMOVEFILTERS
Additional details on these options are available.
Sample Size Weighted Meta-analysis
WEIGHTLABEL [LABEL] (default = 'N') PVALUELABEL [LABEL] (default = 'PVALUE') DEFAULTWEIGHT [NUMBER] (default = 1.0) MINWEIGHT [NUMBER] (default = 1.0)
Inverse Variance Weighted Meta-analysis
STDERRLABEL [LABEL] (default = 'STDERR') SCHEME [SAMPLESIZE|STDERR] (default = SAMPLESIZE)
Tracking of Allele Frequencies
AVERAGEFREQ [ON|OFF] (default = OFF) MINMAXFREQ [ON|OFF] (default = OFF) FREQLABEL [LABEL] (default = 'FREQ')
User Defined Variables
CUSTOMVARIABLE [VARNAME] LABEL [VARNAME] AS [HEADER]
Additional details on these options are available.
Explicit Strand Information
USESTRAND [ON|OFF] (default = OFF) STRANDLABEL [LABEL] (default = 'STRAND')
Genomic Control Correction of Input Statistics
GENOMICCONTROL [ON|OFF|VALUE|LIST snps.txt](default = OFF)
Additional details on this option are available.
General Analysis Control
PROCESSFILE [FILENAME] OUTFILE [PREFIX SUFFIX] (default = 'METAANALYSIS','.TBL') MAXWARNINGS [NUMBER] (default = 20) VERBOSE [ON|OFF] (default = 'OFF') LOGPVALUE [ON|OFF] (default = 'OFF') ANALYZE [HETEROGENEITY] CLEAR
Additional details on the LogPValue and Verbose commands are available.
Script Control
SOURCE [FILENAME]
Additional details on this command are available.