IMPACT_query: Query IMPACT annotations

In RajLabMSSM/echoannot: echoverse module: Annotate fine-mapping results

Query IMPACT annotations

Description

Query annotations/LD-scores generated by IMPACT (Inference and Modeling of Phenotype-related ACtive Transcription), IMPACT predicts transcription factor (TF) binding at a motif site by learning the epigenomic profiles at those sites (primarily ENCODE). All data are aligned to the hg19 genome build. All data has also been reformatted to tabix indexed files and uploaded to Zenodo here to allow for rapid querying.

Usage

IMPACT_query(
  query_dat,
  types = c("annot", "ldscore"),
  populations = c("EAS", "EUR"),
  query_genome = "hg19",
  target_genome = "hg19",
  overlapping_only = TRUE,
  output_format = c("wide", "long", "list"),
  add_metadata = FALSE,
  conda_env = "echoR_mini",
  nThread = 1,
  verbose = TRUE
)

Arguments

query_dat	Variant-level summary statistics.
types	File types to include.
populations	Population ancestries to include ("EAS" = East Asian; "EUR" = European).
query_genome	Genome build that the query_granges is aligned to.
target_genome	Genome build of the VCF file.
overlapping_only	Remove variants that do not overlap with the positions in query_dat.
output_format	Output format options: "wide" : Spread annotation across columns and keep 1 row/SNP. "long" : Melt annotation across rows and allow multiple rows/SNP. "list" : Do not perform merging of queries and instead return results as a named list, where the name is the file the annotation came from.
add_metadata	Add metadata about each sample (Warning: can substantially increase the dataset size).
conda_env	Conda environments to search in. If NULL (default), will search all conda environments.
nThread	Number of threads to use.
verbose	Print messages.

Value

A named list or data.table of annotations merged with query_dat.

Examples

query_dat <- echodata::BST1[1:50,]
annot_dt <- IMPACT_query(query_dat=query_dat, populations="EUR")

RajLabMSSM/echoannot documentation built on Oct. 26, 2023, 2:41 p.m.