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Revision as of 13:53, 7 August 2013
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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 [[METAL COLUMNCOUNTING|COLUMNCOUNTING]] and [[METAL EFFECTLABEL|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 [[METAL ADDFILTER|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 [[METAL CUSTOMVARIABLE|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 [[METAL GENOMICCONTROL|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 [[METAL LOGPVALUE|LogPValue]] and [[METAL VERBOSE|Verbose]] commands are available.
=== Script Control ===
SOURCE [FILENAME]
Additional details on this command are [[METAL SOURCE|available]].
