Annotate_Single_Variants: Functionally annotate a list of variants

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

Functionally annotate a list of variants

Description

The Annotate_Single_Variants function takes in a list of variants to functionally annotate the input variants

Usage

Annotate_Single_Variants(
  agds_dir,
  single_variants_list,
  QC_label = "annotation/filter",
  Annotation_dir = "annotation/info/FunctionalAnnotation",
  Annotation_name_catalog,
  Annotation_name
)

Arguments

agds_dir	file directory of annotated GDS (aGDS) files for all chromosomes (1-22).
single_variants_list	a data frame containing the information of variants to be functionally annotated. The data frame must include 4 columns with the following names: "CHR" (chromosome number), "POS" (position), "REF" (reference allele), and "ALT" (alternative allele).
QC_label	channel name of the QC label in the GDS/aGDS file (default = "annotation/filter").
Annotation_dir	channel name of the annotations in the aGDS file (default = "annotation/info/FunctionalAnnotation").
Annotation_name_catalog	a data frame containing the annotation names and the corresponding channel names 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) and annotation scores for the input variants.

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 July 27, 2024, 4:30 p.m.