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RAREMETAL Command Reference

2,670 bytes added, 13:53, 7 August 2013
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to be constructed === 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]].

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