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Run Nominal Cis-QTL Mapping (CACTI-S)

Source: R/step_s_map_cis.R
cacti_s_map_cis.Rd

Performs linear regression using MatrixEQTL to generate summary statistics.

Usage

cacti_s_map_cis(
  file_pheno,
  file_pheno_meta,
  file_cov,
  file_qtl_out,
  file_vcf = NULL,
  file_geno = NULL,
  file_snp_pos = NULL,
  cis_dist = 1e+05,
  p_threshold = 1
)

Arguments

file_pheno

Path to the processed phenotype file with position meta and expression data (from cacti_s_preprocess).

file_pheno_meta

Path for the meta file of processed phenotype.

file_cov

Path to covariate matrix.

file_qtl_out

Output path for summary statistics.

file_vcf

Path to input VCF file.

file_geno

(Optional) Path to genotype matrix if no VCF.

file_snp_pos

(Optional) Path to SNP positions if no VCF.

cis_dist

Cis-window distance (default 100000 bp = 100kb).

p_threshold

P-value threshold for output (default 1.0, print all associations).

Value

Invisibly returns the summary stats.

Examples

if (FALSE) { # \dontrun{
# Use local paths for testing
file_pheno <- "inst/extdata/test_results/test_pheno_norm.txt"
file_pheno_meta <- "inst/extdata/test_results/test_pheno_norm_meta.txt"
file_cov   <- "inst/extdata/test_cov.txt"
file_vcf   <- "inst/extdata/test_geno.vcf"

file_out <- "inst/extdata/test_results/test_cis_qtl_stats.txt"

# Run
if (file.exists(file_pheno) && file.exists(file_vcf)) {
  cacti_s_map_cis(
    file_pheno   = file_pheno,
    file_pheno_meta = file_pheno_meta,
    file_cov     = file_cov,
    file_vcf     = file_vcf,
    file_qtl_out = file_out,
    cis_dist     = 100000
  )
}
} # }