MetaSKAT_MSSD_OneSet: Meta analysis SKAT with summary data from each study cohort.

Description Usage Arguments Details Value Author(s) References

View source: R/Meta_SKAT.R

Description

Meta analysis SKAT with Meta SSD (MSSD) and Info (MInfo) files. MetaSKAT_MSSD_OneSet computes a p-value for a given set, and MetaSKAT_MSSD_ALL computes p-values for all sets.

Usage

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MetaSKAT_MSSD_OneSet(Cohort.Info, SetID, combined.weight=TRUE, weights.beta=c(1,25),
method="davies", r.corr=0, is.separate = FALSE, Group_Idx=NULL, MAF.cutoff=1, 
missing_cutoff=0.15)

MetaSKAT_MSSD_ALL(Cohort.Info, ...)

 

Arguments

Cohort.Info

output object from Open_MSSD_File_2Read.

SetID

a character value of set id to test.

combined.weight

a logical value (default=TRUE) for a type of weighting. See MetaSKAT_wZ page for details.

weights.beta

a numeric vector of parameters for the beta weights (default=c(1,25))

method

a method to compute a p-value (default= "davies"). See MetaSKAT_wZ page for details.

r.corr

the ρ parameter for the compound symmetric correlation structure kernels (default= 0). See MetaSKAT_wZ page for details.

is.separate

a logical value (default=FALSE) for homogeneous(=FALSE) or heterogeneous(=TRUE) genetic effects of a SNP set across studies. See MetaSKAT_wZ page for details.

Group_Idx

a vector of group indicator (default=NULL). See MetaSKAT_wZ page for details.

MAF.cutoff

a cutoff of the MAFs of SNPs (default=1). Any SNPs with MAFs > MAF.cutoff will be excluded from the analysis.

missing_cutoff

a cutoff of the missing rates of SNPs (default=0.15). See MetaSKAT_wZ page for details.

...

the same parameters of MetaSKAT_MSSD_OneSet after SetID.

Details

Please see MetaSKAT_wZ for details.

Value

MetaSKAT_MSSD_OneSet and MetaSKAT_wZ return the same object. See MetaSKAT_wZ for details. MetaSKAT_MSSD_ALL returns a dataframe with SetIDs (first column) and p-values (second column).

Author(s)

Seunggeun Lee

References

Lee, S., Teslovich, T., Boehnke, M., Lin, X. (2013) General framework for meta-analysis of rare variants in sequencing association studies. American Journal of Human Genetics, 93, 42-53.


MetaSKAT documentation built on May 29, 2017, 2:01 p.m.