simulateConfInt: Simulation of delta SPP index confidence intervals

In bmansfeld/QTLseqr: QTL mapping using Bulk Segregant Analysis of Next Generation Sequencing data.

Description

The method for simulating delta SNP-index confidence interval thresholds as described in Takagi et al., (2013). Genotypes are randomly assigned for each indvidual in the bulk, based on the population structure. The total alternative allele frequency in each bulk is calculated at each depth used to simulate delta SNP-indeces, with a user defined number of bootstrapped replication. The requested confidence intervals are then calculated from the bootstraps.

Usage

simulateConfInt(popStruc = "F2", bulkSize, depth = 1:100,
  replications = 10000, filter = 0.3, intervals = c(0.05, 0.025))

Arguments

popStruc	the population structure. Defaults to "F2" and assumes "RIL"
bulkSize	non-negative integer vector. The number of individuals in each simulated bulk. Can be of length 1, then both bulks are set to the same size. Assumes the first value in the vector is the simulated high bulk.
depth	integer. A read depth for which to replicate SNP-index calls.
replications	integer. The number of bootstrap replications.
filter	numeric. An optional minimum SNP-index filter
intervals	numeric vector of probabilities with values in [0,1] corresponding to the requested confidence intervals

Value

A data frame of delta SNP-index thresholds corrisponding to the requested confidence intervals at the user set depths.

Examples

CI <-
simulateConfInt(
   popStruc = "F2",
   bulkSize = 50,
   depth = 1:100,
   intervals = c(0.05, 0.95, 0.025, 0.975, 0.005, 0.995, 0.0025, 0.9975)

bmansfeld/QTLseqr documentation built on Jan. 24, 2020, 3:56 p.m.