Burden_Effect_Size_meta: Effect size and standard error estimates of meta-analysis of...

In xihaoli/MetaSTAAR: Meta-Analysis of STAAR (MetaSTAAR) Procedure for Dynamic Incorporation of Multiple Functional Annotations in Whole Genome Sequencing Studies

Effect size and standard error estimates of meta-analysis of burden test for a given variant-set

Description

The Burden_Effect_Size_meta function takes in the object from the merged summary statistics and covariance files of each participating study and functional annotation data to calculate the effect size and standard error estimates of meta-analysis of burden test for a given variant-set.

Usage

Burden_Effect_Size_meta(obj_MetaSTAAR_merge, rv_num_cutoff = 2)

Arguments

obj_MetaSTAAR_merge	an object from merging the summary statistics and covariance files from each participating study, which is the output from MetaSTAAR_merge.
rv_num_cutoff	the cutoff of minimum number of variants of analyzing a given variant-set (default = 2).

Value

a list with the following members:

num_variant: the number of variants with combined minor allele frequency > 0 and less than rare_maf_cutoff in the given variant-set that are used for performing the variant-set test using MetaSTAAR.

cMAC: the combined cumulative minor allele count of variants with combined minor allele frequency > 0 and less than rare_maf_cutoff in the given variant-set.

Burden_Score_Stat: the score statistic of Burden-MS(1,1) for the given variant-set.

Burden_SE_Score: the standard error of Burden_Score_Stat for the given variant-set.

Burden_pvalue: the Burden-MS(1,1) p-value for the given variant-set.

Burden_Est: the effect size estimate of Burden-MS(1,1) for the given variant-set.

Burden_SE_Est: the standard error estimate of Burden_Est for the given variant-set.

References

Li, X., et al. (2023). Powerful, scalable and resource-efficient meta-analysis of rare variant associations in large whole genome sequencing studies. Nature Genetics, 55(1), 154-164. (pub)

xihaoli/MetaSTAAR documentation built on Nov. 10, 2024, 5:26 a.m.