process.eqtl.input: Process eQTL input
In josefin-werme/LAVA: Local Analysis of [co]Variant Association

process.eqtl.input

R Documentation

Process eQTL input

Description

Modifies the GWAS input object, appending eQTL (or sQTL) summary statistics and gene annotation to an existing GWAS input. See https://ctg.cncr.nl/software/lava for preformatted GTEx v8 input files and details on the formatting of the input files.

Usage

process.eqtl.input(
  gwas.input,
  eqtl.folder,
  prefix = "gtex_v8",
  tissue = NULL,
  chromosomes = "all"
)

Arguments

`gwas.input`	GWAS input object generated using `process.input` (object is modified by function).
`eqtl.folder`	Folder containing the eQTL input files (format described in link above).
`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 (the X chromosome can be specified as 'X' or 23).
`file.prefix`	Prefix of primary input files.

Value

No return value, the gwas.input argument is modified in place. An 'eqtl' phenotype is added to the existing gwas.input structure, and the following fields are added. 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
current.stats - summary statistics for the currently loaded tissue