| MetaSKAT_MSSD_OneSet {MetaSKAT} | R Documentation |
Meta analysis SKAT with summary data from each study cohort.
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
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 |
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.