Indiv_Score_Test_Region_meta_cond: Meta-analysis of conditional score test for individual...
In xihaoli/MetaSTAAR: Meta-Analysis of STAAR (MetaSTAAR) Procedure for Dynamic Incorporation of Multiple Functional Annotations in Whole Genome Sequencing Studies
View source: R/Indiv_Score_Test_Region_meta_cond.R
Indiv_Score_Test_Region_meta_cond R Documentation
Meta-analysis of conditional score test for individual variants in a given variant-set
Description
The Indiv_Score_Test_Region_meta_cond function takes in the object from the
merged conditional summary statistics and covariance files of each participating study to analyze
the conditional associations between a quantitative/dichotomous phenotype and
all individual variants in a given variant-set by using the meta-analysis of score test,
adjusting for a given list of variants.
Usage
Indiv_Score_Test_Region_meta_cond(obj_MetaSTAAR_merge_cond, rv_num_cutoff = 2)
Arguments
obj_MetaSTAAR_merge_cond
an object from merging the conditional summary statistics
and covariance files from each participating study, adjusting for a given list of variants,
which is the output from MetaSTAAR_merge_cond.
rv_num_cutoff
the cutoff of minimum number of variants of analyzing
a given variant-set (default = 2).
Value
a data frame with p rows corresponding to the p genetic variants in the given variant-set
and three columns: Score_cond (the conditional score test statistic),
SE_cond (the standard error associated with the conditional score test statistic),
and pvalue_cond (the conditional score test p-value). If a variant in
the given variant-set has standard error equal to 0, the p-value will be set as 1.
xihaoli/MetaSTAAR documentation built on Nov. 10, 2024, 5:26 a.m.
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View source: R/Indiv_Score_Test_Region_meta_cond.R
| Indiv_Score_Test_Region_meta_cond | R Documentation |
Meta-analysis of conditional score test for individual variants in a given variant-set
Description
The Indiv_Score_Test_Region_meta_cond function takes in the object from the
merged conditional summary statistics and covariance files of each participating study to analyze
the conditional associations between a quantitative/dichotomous phenotype and
all individual variants in a given variant-set by using the meta-analysis of score test,
adjusting for a given list of variants.
Usage
Indiv_Score_Test_Region_meta_cond(obj_MetaSTAAR_merge_cond, rv_num_cutoff = 2)
Arguments
obj_MetaSTAAR_merge_cond |
an object from merging the conditional summary statistics
and covariance files from each participating study, adjusting for a given list of variants,
which is the output from |
rv_num_cutoff |
the cutoff of minimum number of variants of analyzing a given variant-set (default = 2). |
Value
a data frame with p rows corresponding to the p genetic variants in the given variant-set
and three columns: Score_cond (the conditional score test statistic),
SE_cond (the standard error associated with the conditional score test statistic),
and pvalue_cond (the conditional score test p-value). If a variant in
the given variant-set has standard error equal to 0, the p-value will be set as 1.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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