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| | ==PhoneHome== | | ==PhoneHome== |
| − | ===--noPhoneHome===
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| − | ===--phoneHomeThinning===
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| − | | + | {{PhoneHomeParameters|hdr===|bullet=1}} |
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| − | * --prefix is optional.
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| − | * If --prefix is not specified, the output file names will be:
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| − | traitname.singlevar.score.txt
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| − | traitname.singlevar.cov.txt
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| − | * Otherwise, the output file names are:
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| − | prefix.traitname.singlevar.score.txt
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| − | prefix.traitname.singlevar.cov.txt
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| − | * --LDwindow specifies the length of the window that LD Matrix should be generated upon each variant. The default is 1MB.
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| − | * --zip gives users the option of writing compressed files (bgzip compressed) automatically for convenient sharing.
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| − | * --thin tells RMW to thin points when generating QQ plot and Manhattan plots, so the file size is smaller.
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| − | * --labelHits tells RMW to to label the hits using pvalue threshold 0.05/(#of variants tested) with gene name, based on human genome build 19.
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| − | ==== VC Options ====
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| − | * When --vcShared and --vcX are specified, RMW knows that you want to fit shared environment and/or chromosome X variance component together with genetic component and non-shared environment.
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| − | * When --makeResiduals is specified, RMW understands covariates should be read from PED/DAT file. Covariates are modeled as fixed effects.
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| − | ==== Trait Options ====
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| − | * --makeResiduals tells RMW to adjust the covariates and analyze residuals instead of the original phenotypes. If either --kinGeno or --kinPedigree option is used, then a variance component model will be fit based on residuals. If the --inverseNormal option is also used, then the residuals will be quantile normalized before fitting variance component model.
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| − | * --traitName is created for situations when you have many traits saved in your PED and DAT file, but you are interested in one or a few of them. It can read a file ending with .txt with each trait of interest in a separate line, or trait names separated with "/". An example to handle one trait or multiple traits is in the following:
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| − | --traitName LDL
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| − | --traitName LDL/HDL/TG
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| − | --traitName traitsOfInterest.txt
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| − | * If --traitName is not used, all traits in PED/DAT file will be analyzed.
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| − | | |
| − | ==== Model Options ====
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| − | * additive model is used in RMW as default.
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| − | * --recessive allows additional association results (pvalue, effect size, and standard error) generated using recessive model. If VCF file is used, then non-reference allele is considered the recessive allele. If PED/DAT files are used for genotype, then minor allele is considered the recessive allele.
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| − | * --dominant allows additional association results (pvalue, effect size, and standard error) generated using dominant model. If VCF file is used, then non-reference allele is considered the dominant allele. If PED/DAT files are used for genotype, then minor allele is considered the dominant allele.
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| − | * --recessive and --dominant options can be used together.
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| − | * Recessive and dominant results are stored in separate files.
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| − | ==== Kinship Source ====
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| − | * --kinPedigree allows RMW to generate kinship matrix from pedigree, when pedigree information is available.
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| − | * --kinGeno informs RMW to generate kinship matrix from all available variants that pass the criteria, specified in --kinMaf and --kinMiss options. The default will take variants with MAF>0.05 and genotype missing rate <0.05.
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| − | * --kinGeno option can NOT be used with --kinPedigree or --kinFile option. Only one of three options or none of them can be used in the same run.
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| − | * --kinFile let RMW read in a kinship matrix from a file. The first row of the kinship file has to be the sample IDs included in the kinship file. If a sample of interest is not included in the kinship file, fatal error will occur and the program will be terminated. A sample of interest is a sample that is phenotyped and has all covariates measured when --makeResiduals is specified.
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| − | * --kinSave allows you to save the kinship matrix.
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| − | ==== Kinship Options ====
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| − | * --kinMiss and --kinMaf should be used with --kinGeno together.
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| − | * --kinMiss specifies the maximum genotype missing rate when calculating kinship from genotypes. The default is 0.05.
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| − | * --kinMaf specifies the minimum minor allele frequency used when calculating kinship from genotypes. The default is 0.05.
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| − | ==== Chromosome X ====
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| − | * --xLabel should have a value of a string which specifies how variants on chromosome X are coded. The default is "X".
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| − | * --xStart and --xEnd specifies the start and end of non-pseudo-autosomal regions on chromosome X. These options should be specified when --vcX is used.
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| − | * The default for --xStart is 2699520 and default for --xEnd is 154931044, according to NCBI genome build 37.
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| − | Please refer to the following for the analysis of X-linked variants [[RAREMETALWORKER_X|'''ANALYZING CHROMOSOME X''']].
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| − | {{PhoneHomeParameters|hdr=====|bullet=1}} | |
