eqtl_simulator_cistrans_h5: Simulating eQTL phenotypes.

In jinhyunju/eQTLtools: What the package does (one line)

Description

Generates a phenotype matrix based on a given input genotype matrix.

Usage

eqtl_simulator_cistrans_h5(input_h5 = NULL, n_pheno = 2000, n_geno = NULL,
  n_eqtl = 1500, cis_trans_ratio = 0.7, simulation.id = "sim1",
  output.path = "./", coeff_mean = 2.5, trans_nerf = 0.7, hot_spots = 8,
  hot_spot_impact = 0.1, hidden.factor = TRUE, factors = "sparse",
  factor_coeff = 2.1, hf_frac = 0.2, effect_size = 2,
  factor_type = "sparse")

Arguments

genotypes	A genotype matrix with dimensions N x g.
n.pheno	Number of phenotypes to simulate
n.eqtl	Number of eQTL pairs
cis.trans.ratio	Ratio between cis and trans hits
trans.impact	Maximum percentage of total genes a trans hit can influence.
trans.nerf	Ratio of trans effect size compared to cis-hits. Accounts for the observation that trans hits usually have smaller effect sizes.
coeff.sample	A vector from which the effect sizes (coefficiens) are going to be sampled from.

Value

Phenotype matrix with dimensions N x n.pheno

jinhyunju/eQTLtools documentation built on May 19, 2019, 10:35 a.m.