process.eqtl.input: Process eQTL input from text input files

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

Process eQTL input from text input files

Description

Modifies the GWAS input object, appending eQTL (or sQTL) summary statistics and gene annotation to an existing GWAS input from plain-text input files. Input files should follow the same format as summary statistics input files for other phenotypes, with an additional column GENE to indicate which gene the association results on each line belong to. Input files must be provided separately per chromosome.

Usage

process.eqtl.input(
  gwas.input,
  eqtl.file.spec,
  chromosomes = "all",
  sample.size = NULL
)

Arguments

gwas.input	GWAS input object generated using process.input (object is modified by function).
eqtl.file.spec	File name specifier for eQTL summary statistics input files, with a placeholder [CHR] to indicate the chromosome number in the file name; eg. "my_folder/eqtl.chr[CHR].stats"
chromosomes	Specifies which chromosomes to load the 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).
sample.size	If set, used as sample size value for each SNP in the input files instead of N column.

Value

No return value, the gwas.input argument is modified in place. An 'eqtl' phenotype is added into the existing gwas.input structure, and the following fields are added to gwas.input.

• current.chromosomes - list of currently loaded chromosomes

• current.genes - vector of available genes

• current.stats - summary statistics for all loaded genes

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