Difference between revisions of "RAREMETAL Command Reference"

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

Revision as of 13:53, 7 August 2013

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.