Difference between revisions of "RAREMETAL Command Reference"
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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.
