compute_SNPSEA_enrichment_linear: Compute SNPsea enrichment linear

In alexandruioanvoda/gwascelltyper: Fast GWAS Enrichment Testing

Compute SNPsea enrichment linear

Description

Compute GWAS enrichment in gene specificity matrices (linear analysis) with SNPsea.

Usage

compute_SNPSEA_enrichment_linear(
  gene_score_matrix,
  sumstats_file,
  output_dir = NULL,
  number_of_threads = 1,
  slop = "10e3",
  null_snpsets = 0,
  min_observations = 100,
  max_iterations = "1e7",
  gene_nomenclature = "hgnc",
  snpsea_path = paste0(system.file(package = "gwascelltyper"),
    "/extdata/snpsea-linux64"),
  gene_intervals = paste0(system.file(package = "gwascelltyper"),
    "/extdata/NCBIgenes2013_", gene_nomenclature, ".bed.gz"),
  snp_intervals = paste0(system.file(package = "gwascelltyper"),
    "/extdata/TGP2011.bed.gz"),
  null_snps = paste0(system.file(package = "gwascelltyper"),
    "/extdata/Lango2010.txt.gz")
)

Arguments

gene_score_matrix	Matrix with HGNC genes as rows & cell-types as columns. Values need to be numeric.
sumstats_file	Address of properly formatted SNPsea GWAS file.
output_dir	Folder where you want the output to be stored. Default = NULL, which makes this function create a directory where results will be temporarily stored. The directory will be deleted afterwards, if this parameter is null. The only output will be the return. Otherwise, both the files and the return are kept.
number_of_threads	Number of threads to parallelize calculation over (default = 1).
slop	If a SNP overlaps no gene intervals, extend the SNP interval this many nucleotides further and try again (default: 10000).
null_snpsets	Generate a distribution of scores with N null matched SNP sets to evaluate type 1 error (default: 0).
min_observations	Stop testing a column in –gene-matrix after observing this many null SNP sets with specificity scores greater or equal to those obtained with the SNPs in –snps. Increase this value to obtain more accurate p-values (default: 25).
max_iterations	Maximum number of null SNP sets tested against each column in –gene-matrix. Increase this value to resolve small p-values (default: 10000).
gene_nomenclature	Type of gene names.
snpsea_path	Path to the SNPsea executable
gene_intervals	BED file with gene intervals. The fourth column must contain the same gene identifiers as in –gene-matrix.
snp_intervals	BED file with all known SNP intervals. The fourth column must contain the same SNP identifiers as in –snps and –null-snps.
null_snps	Text file with SNP identifiers to sample when generating null matched or random SNP sets. These SNPs must be a subset of –snp-intervals.

Value

Dataframe

alexandruioanvoda/gwascelltyper documentation built on April 16, 2023, 8:03 p.m.