MetaSTAAR_individual_analysis: Meta-analysis of individual variants using 'MetaSTAAR'

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

Meta-analysis of individual variants using MetaSTAAR

Description

The MetaSTAAR_individual_analysis function takes in the summary statistics file from each participating study (the output from MetaSTAAR_worker_sumstat) to analyze the associations between a quantitative/dichotomous phenotype and all individual variants in the merged variant list by using the meta-analysis of score test.

Usage

MetaSTAAR_individual_analysis(
  chr,
  start.loc,
  end.loc,
  study.names,
  sample.sizes,
  sumstat.dir,
  common_mac_cutoff,
  trait,
  segment.size = 5e+05,
  check_qc_label = FALSE
)

Arguments

chr	a numeric value indicating the chromosome of the genetic region of interest.
start.loc	a numeric value indicating the starting location (position) of the genetic region of interest.
end.loc	a numeric value indicating the ending location (position) of the genetic region of interest.
study.names	a character vector containing the name of each participating study in the meta-analysis.
sample.sizes	a numeric vector with the length of study.names indicating the sample size of each study.
sumstat.dir	a character vector containing the directories of the study-specific summary statistics file folders.
common_mac_cutoff	the cutoff of minimum combined minor allele count (inclusive) in defining "common" variants.
trait	a character value indicating the underlying trait of interest for the meta-analysis.
segment.size	a numeric value indicating the length of each segment of which the summary statistics and sparse weighted covariance files are stored. Note that the input value should be aligned with the input values of MetaSTAAR_worker_cov (default = 5e+05).
check_qc_label	a logical value indicating whether variants need to be dropped according to qc_label specified in MetaSTAAR_worker_sumstat and MetaSTAAR_worker_cov. If check_qc_label is FALSE, it is assumed that no variant will be dropped (default = FALSE).

Value

a data frame with p rows corresponding to the p genetic variants in the merged variant list and the following columns: chromosome (chr), position (pos), reference allele (ref), alternative allele (alt), combined alternative allele count (alt_AC), combined minor allele count (MAC), combined minor allele frequency (MAF), combined sample size (N), the score test p-value (p), the log score test p-value (logp), the score test statistic (Score), the standard error associated with the score test statistic (Score_SE), the estimated effect size of the minor allele (Est), the standard error associated with the estimated effect size (Est_se). If a variant in the merged variant list has standard error equal to 0, the p-value will be set as 1.

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.