runQTLseqAnalysis: Calculates delta SNP confidence intervals for QTLseq analysis

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

runQTLseqAnalysis(SNPset, windowSize = 1e+06, popStruc = "F2",
  bulkSize, depth = NULL, replications = 10000, filter = 0.3,
  intervals = c(95, 99), ...)

Arguments

SNPset	The data frame imported by ImportFromGATK
windowSize	the window size (in base pairs) bracketing each SNP for which to calculate the statitics.
popStruc	the population structure. Defaults to "F2" and assumes "RIL" otherwise
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. Confidence intervals supplied as two-sided percentiles. i.e. If intervals = '95' will return the two sided 95% confidence interval, 2.5% on each side.
...	Other arguments passed to locfit and subsequently to locfit.raw() (or the lfproc). Usefull in cases where you get "out of vertex space warnings"; Set the maxk higher than the default 100. See locfit.raw(). But if you are getting that warning you should seriously consider increasing your window size.

Value

A SNPset data frame with delta SNP-index thresholds corrisponding to the requested confidence intervals matching the tricube smoothed depth at each SNP.

Examples

df_filt <- runQTLseqAnalysis(
SNPset = df_filt,
bulkSize = c(25, 35)
windowSize = 1e6,
popStruc = "F2",
replications = 10000,
intervals = c(95, 99)
)

bmansfeld/QTLseqR documentation built on Jan. 25, 2020, 8:52 p.m.