mixqtl: Combining total and allele-specific reads for QTL mapping

In liangyy/mixqtl: Combine total and allele-specific counts for cis-QTL analysis

Description

Given total and allele-specific read counts along with library size, MixQTL procedure (by meta-analysis) is implemented. Specifically, first, ascQTL and trcQTL estimates are obtained. Then, second, meta-analyze ascQTL and trcQTL estimates to obtain mixQTL estimate. The function outputs the estimates of outcome versus each of the input variants

Usage

mixqtl(
  geno1,
  geno2,
  y1,
  y2,
  ytotal,
  lib_size,
  cov_offset = NULL,
  trc_cutoff = 20,
  asc_cutoff = 5,
  weight_cap = 100,
  asc_cap = 5000
)

Arguments

geno1	genotype of haplotype 1 (dimension = N x P)
geno2	genotype of haplotype 2 (dimension = N x P)
y1	allele-specific read count for haplotype 1 (dimension = N x 1)
y2	allele-specific read count for haplotype 2 (dimension = N x 1)
ytotal	total read count (dimension = N x 1)
lib_size	library size (dimension = N x 1)
cov_offset	predicted effect of covariates on total read count response term, log(ytotal / lib_size / 2) (dimension = N x 1)
trc_cutoff	total read count cutoff to exclude observations with ytotal lower than the cutoff
asc_cutoff	allele-specific read count cutoff to exclude observations with y1 or y2 lower than asc_cutoff
weight_cap	the maximum weight difference (in fold) is min(weight_cap, floor(sample_size / 10)). The ones exceeding the cutoff is capped.
asc_cap	exclude observations with y1 or y2 higher than asc_cap

Value

QTL mapping result

Examples

mixqtl(
  geno1 = matrix(sample(c(0, 0.5, 1), 200, replace = TRUE), ncol = 2),
  geno2 = matrix(sample(c(0, 0.5, 1), 200, replace = TRUE), ncol = 2),
  y1 = rpois(100, 100),
  y2 = rpois(100, 100),
  ytotal = rpois(100, 1000),
  lib_size = rpois(100, 10000),
  cov_offset = runif(100),
  trc_cutoff = 100,
  asc_cutoff = 50,
  weight_cap = 100,
  asc_cap = 1000
)

liangyy/mixqtl documentation built on Sept. 17, 2020, 11:36 a.m.