Difference between revisions of "METAL Command Reference"
From Genome Analysis Wiki
Jump to navigationJump to search(7 intermediate revisions by the same user not shown) | |||
Line 7: | Line 7: | ||
FLIP | FLIP | ||
− | Additional details on the [[METAL COLUMNCOUNTING|COLUMNCOUNTING]] | + | Additional details on the [[METAL COLUMNCOUNTING|COLUMNCOUNTING]] and [[METAL EFFECTLABEL|EFFECTLABEL]] options are available. |
=== Filtering Input Files === | === Filtering Input Files === | ||
Line 13: | Line 13: | ||
(available conditions are <, >, <=, >=, =, !=, IN) | (available conditions are <, >, <=, >=, =, !=, IN) | ||
REMOVEFILTERS | REMOVEFILTERS | ||
+ | |||
+ | Additional details on these options are [[METAL ADDFILTER|available]]. | ||
=== Sample Size Weighted Meta-analysis === | === Sample Size Weighted Meta-analysis === | ||
Line 32: | Line 34: | ||
CUSTOMVARIABLE [VARNAME] | CUSTOMVARIABLE [VARNAME] | ||
LABEL [VARNAME] AS [HEADER] | LABEL [VARNAME] AS [HEADER] | ||
+ | |||
+ | Additional details on these options are [[METAL CUSTOMVARIABLE|available]]. | ||
=== Explicit Strand Information === | === Explicit Strand Information === | ||
Line 38: | Line 42: | ||
=== Genomic Control Correction of Input Statistics === | === Genomic Control Correction of Input Statistics === | ||
− | GENOMICCONTROL [ON|OFF|VALUE] | + | GENOMICCONTROL [ON|OFF|VALUE|LIST snps.txt](default = OFF) |
+ | |||
+ | Additional details on this option are [[METAL GENOMICCONTROL|available]]. | ||
=== General Analysis Control === | === General Analysis Control === | ||
Line 48: | Line 54: | ||
ANALYZE [HETEROGENEITY] | ANALYZE [HETEROGENEITY] | ||
CLEAR | 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]]. |
Latest revision as of 07:36, 25 March 2011
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.