CSeQTL_full_analysis: CSeQTL_full_analysis

In CSeQTL: Cell Type-Specific Expression Quantitative Trait Loci Mapping

CSeQTL_full_analysis

Description

Performs marginal and cell type-specific eQTL analysis with both CSeQTL and OLS models for simulation and comparative purposes.

Usage

CSeQTL_full_analysis(
  TREC,
  hap2,
  ASREC,
  PHASE,
  SNP,
  RHO,
  XX,
  log_lib_size,
  vec_MARG = c(TRUE, FALSE),
  vec_TRIM = c(TRUE, FALSE),
  vec_PERM = c(TRUE, FALSE),
  thres_TRIM = 10,
  ncores = 1,
  show = TRUE
)

Arguments

TREC	An integer vector of total read counts.
hap2	An integer vector of second haplotype counts
ASREC	An integer vector of total haplotype counts
PHASE	An integer vector of 0s and 1s denoting if a subject has available haplotype counts.
SNP	An integer vector of phased genotypes coded 0 (AA), 1 (AB), 2 (BA), 3 (BB), and 5 (NA).
RHO	A numeric matrix of cell type proportions. Rows correspond to subjects and columns correspond to cell types.
XX	A numeric design matrix of baseline covariates including the intercept in the first column and centered continuous covariates.
log_lib_size	A positive numeric vector of log transformed library sizes per subject.
vec_MARG	A boolean vector for marginal and/or cell type-specific analyses to be run. By default, both sets of analyses are run.
vec_TRIM	A boolean vector for whether or not analyses with trimmed outcomes are included. By default, both sets of analyses are run.
vec_PERM	A boolean vector for whether or not permuted SNP analyses are included. By default, both sets of analyses are run.
thres_TRIM	A positive numeric value to perform subject outcome trimming. Subjects with standardized Cooks' Distances greater than the threshold are trimmed.
ncores	A positive integer specifying the number of threads available to decrease computational runtime.
show	A boolean value to display verbose output and plot intermediate simulated results.

Value

A R list containing multiple objects. res is a R dataframe containing the model fitted, marginal model indicator, TRIM indicator, permutation indicator, cell types, utilized allele-specific reads indicator, A and B allele-specific expression, eta/eqtl fold change estimate, p-value. out contains lists of detailed estimates per model fit.

CSeQTL documentation built on April 24, 2026, 9:06 a.m.