Gene_Centric_Coding_Info: Functionally annotate rare variants in a coding mask

In xihaoli/STAARpipelineSummary: Summarization and Visualization of Analysis Results Generated by STAARpipeline

Functionally annotate rare variants in a coding mask

Description

The Gene_Centric_Coding_Info function takes in a coding mask of a gene to functionally annotate the rare variants in the mask.

Usage

Gene_Centric_Coding_Info(
  category = c("plof", "plof_ds", "missense", "disruptive_missense", "synonymous", "ptv",
    "ptv_ds"),
  chr,
  genofile,
  obj_nullmodel,
  gene_name,
  known_loci = NULL,
  rare_maf_cutoff = 0.01,
  method_cond = c("optimal", "naive"),
  QC_label = "annotation/filter",
  variant_type = c("SNV", "Indel", "variant"),
  geno_missing_imputation = c("mean", "minor"),
  Annotation_dir = "annotation/info/FunctionalAnnotation",
  Annotation_name_catalog,
  Annotation_name
)

Arguments

category	the coding functional category of rare variants to be functionally annotated. Choices include plof, plof_ds, missense, disruptive_missense, synonymous, ptv, ptv_ds (default = plof).
chr	chromosome.
genofile	an object of opened annotated GDS (aGDS) file.
obj_nullmodel	an object from fitting the null model, which is either the output from fit_nullmodel function in the STAARpipeline package, or the output from fitNullModel function in the GENESIS package and transformed using the genesis2staar_nullmodel function in the STAARpipeline package.
gene_name	name of the gene to be annotated.
known_loci	the data frame of variants to be adjusted for in conditional analysis and should contain 4 columns in the following order: chromosome (CHR), position (POS), reference allele (REF), and alternative allele (ALT) (default = NULL).
rare_maf_cutoff	the cutoff of maximum minor allele frequency in defining rare variants (default = 0.01).
method_cond	a character value indicating the method for conditional analysis. optimal refers to regressing residuals from the null model on known_loci as well as all covariates used in fitting the null model (fully adjusted) and taking the residuals; naive refers to regressing residuals from the null model on known_loci and taking the residuals (default = optimal).
QC_label	channel name of the QC label in the GDS/aGDS file.
variant_type	type of variant included in the conditional analysis. Choices include "SNV", "Indel", or "variant" (default = "SNV").
geno_missing_imputation	method of handling missing genotypes. Either "mean" or "minor" (default = "mean").
Annotation_dir	channel name of the annotations in the aGDS file (default = "annotation/info/FunctionalAnnotation").
Annotation_name_catalog	a data frame containing the name and the corresponding channel name in the aGDS file.
Annotation_name	a vector of qualitative/quantitative annotation names user wants to extract.

Value

A data frame containing the basic information (chromosome, position, reference allele and alternative allele), unconditional and conditional the score test p-values (not provided for imbalanced case-control setting), and annotation scores for the rare variants of the input coding mask.

References

Li, Z., Li, X., et al. (2022). A framework for detecting noncoding rare-variant associations of large-scale whole-genome sequencing studies. Nature Methods, 19(12), 1599-1611. (pub)

xihaoli/STAARpipelineSummary documentation built on Oct. 20, 2024, 9:35 p.m.