RAREMETAL Command Reference: Difference between revisions
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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]]. | |||
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.
