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** direction.meta.single.var.out: Direction of meta-analysis statistics for single variant test. It may be useful for inspecting if any of the variant in the gene have opposite effects etc.
** direction.meta.single.var.out: Direction of meta-analysis statistics for single variant test. It may be useful for inspecting if any of the variant in the gene have opposite effects etc.
** pos.ref.alt.out: Position, reference and alternative alleles for each variant position in the gene
** pos.ref.alt.out: Position, reference and alternative alleles for each variant position in the gene
== Performing conditional analysis for single variant tests ==
* We provide functions for performing single variant conditional meta-analysis. For variants within the sliding window, the conditional analysis is exact, in the sense that they are equal to conditional analysis results obtained using individual level data.
* The following function can be used:
conditional.rareMETALS.single.basic(candidate.variant,score.stat.file,cov.file,known.variant.vec,maf.cutoff,no.boot=0,alternative=c('two.\
sided','greater','less'),alpha=0.05,ix.gold=1,out.digits=4,callrate.cutoff=0,hwe.cutoff=0,gene.file="refFlat_hg19.txt.gz",p.value.known.v\
ariant.vec="N/A",anno.known.variant.vec="N/A",anno.candidate.variant="N/A")
}
* Input parameters are described below:
** candidate variant: the chromosomal position for the candidate variant to be tested, e.g. "1:12345";
** score.stat.file is the vector of file names for single variant score statistics.
** cov.file is the vector of files of covariance matrices for single variant score statistics
** known.variant.vec is the vector of chromosomal positions for known variants. Examples include c("1:12345","1:1234567");
** alternative specifies alternative hypothesis to be tested. The default is two.sided.
** ix.gold is the index to be used for choosing a "gold standard" population, in case flips of alleles are observed, and the gold standard population can be used to correct for the flips
** callrate.cutoff specifies the call rate cutoffs that will be used. All sites with call rates lower than the cutoff will be labelled as missing.
** hwe.cutoff specifies the cutoffs for call rate, All sites with call rate lower than the cutoff will be labeled as missing.
** anno.known.variant.vec: Annotation information for known variant. It is optional. If the annotation is not present, please use "NA". Note that the quotation mark is a must.
** anno.candidate.variant: Annotation information for candidate variant. It is optional and can be ignored
* Output is a dataframe that consist of the following fields:
** pos.single.out: Chromosomal position for candidate variants
** ref.single.out: Referrence allele
** alt.single.out: Alternative allele
** p.value.single.out: P values
** maf.single.out: Minor allele frequencies
** beta1.est.single.out: Estimates of alternative allele effects
** beta1.sd.single.out: Standard deviation for beta estimates
** direction.single.out: Direction of effects
** anno.single.out: Annotation information for candidate variants
** pos.ref.alt.known.single.out: Position/ref/alt alleles for known variants
** p.value.known.single.out: p-values for known variants
** anno.known.single.out: annotation for known variants
