founderNs: Numbers of founder genotypes

Description Usage Arguments Value Author(s)

Description

founderNs calculates the number of founder genotypes represented in the DSPR RILs at a given position.

Usage

1
founderNs(peakChr, peakPos, design, phenotype.dat, id.col)

Arguments

peakChr

character vector of length one. Must be one of the major chromosome arms in the Drosophila genome ('X','2L','2R','3L',or '3R').

peakPos

numeric vector of length one. A position in base pairs in the DSPR position list (every 10kb).

design

a character string. For inbred RIL designs: 'inbredA', 'inbredB'. For cross designs: AAcross, BBcross, or 'ABcross'. A and B refer to the pA and pB set of DSPR RILs.

phenotype.dat

data.frame containing phenotype data. For inbred designs, there must be a column of numeric RIL ids (must be named patRIL). For the ABcross design, there must be both a patRIL and matRIL column specifying the pA and pB RIL ids. Cross designs also require a sex column for correct specification of the genotypes on the X chromosome.

id.col

a character string identifying the name of the column containing unique ids for the samples. e.g. for an inbred design, the patRIL column can be used as the id.

Value

A named numeric vector consisting of the numbers of RILs in the phenotype.dat data.frame with each founder genotype at the given position. A RIl is assigned a founder genotype if the HMM probability is over 0.95. The number of RILs with a heterozygous genotype and an uncertain genotype are also returned.

Author(s)

Elizabeth King (kingeg@missouri.edu)


egking/DSPRqtl documentation built on May 16, 2019, 12:14 a.m.