getSigRegions: Return SNPs in significant regions

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

Description

The function takes a SNP set after calculation of p- and q-values or Takagi confidence intervals and returns a list containing all SNPs with q-values or deltaSNP below a set alpha or confidence intervals, respectively. Each entry in the list is a SNP set data frame in a contiguous region with adjusted pvalues lower than the set false discovery rate alpha.

Usage

getSigRegions(SNPset, method = "Gprime", alpha = 0.05, interval = 99)

Arguments

SNPset	Data frame SNP set containing previously filtered SNPs.
method	either "Gprime" or "QTLseq". The method for detecting significant regions.
alpha	numeric. The required false discovery rate alpha for use with method = "Gprime"
interval	numeric. For use eith method = "QTLseq" The Takagi based confidence interval requested. This will find the column named "CI_\*\*", where \*\* is the requested interval, i.e. 99.

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