process.eqtl.input.preprocessed: Load eQTL input from preprocessed input files

In josefin-werme/lava: Local Analysis of [co]Variant Association

Load eQTL input from preprocessed input files

Description

Modifies the GWAS input object, appending eQTL (or sQTL) summary statistics and gene annotation to an existing GWAS input from preprocessed GTEx v8 input files (see LAVA website).

Usage

process.eqtl.input.preprocessed(
  gwas.input,
  eqtl.folder,
  prefix = ifelse(is.sqtl, "gtex_sqtl_v8", "gtex_v8"),
  tissue = NULL,
  chromosomes = "all",
  is.sqtl = F
)

Arguments

gwas.input	GWAS input object generated using process.input (object is modified by function).
eqtl.folder	Folder containing the preprocessed eQTL input files.
tissue	If set, initializes the input object for analysis of the specified tissue. Equivalent to calling the set.tissue function after running process.eqtl.input().
chromosomes	Specifies which chromosomes to load the annotation data for (loading all chromosomes may be time-consuming). Can be set to 'all' to load all chromosomes, 'auto' to load all autosomal chromosomes, or a vector of chromosome numbers or single chromosome number (the X chromosome can be specified as 'X' or 23).
is.sqtl	Set to true if input consists of sQTL rather than eQTL summary statistics.
file.prefix	Prefix of primary input files.

Value

No return value, the gwas.input argument is modified in place. An 'eqtl' or 'sqtl' phenotype is added into the existing gwas.input structure, and the following fields are added to gwas.input. Note that if the 'tissue' argument is not set, set.tissue must be called on 'gwas.input' to fully initialize the input object for analysis.

• eqtl.files - list of all the file names and folders used

• eqtl.genes - list containing the names and mapped SNPs for all genes in the eQTL data set

• eqtl.tissues - data.frame with all the available tissues

• current.tissue - name of the currently loaded tissue (NULL if not set yet)

• current.chromosomes - list of currently loaded chromosomes

• current.genes - vector of genes available for the currently loaded tissue; for sQTL data, these are gene name + splicing ID combinations rather than individual genes

• current.stats - summary statistics for the currently loaded tissue

josefin-werme/lava documentation built on July 17, 2025, 5:21 a.m.