geno.means: Founder genotype means and standard errors

In egking/DSPRqtl: Analysis of DSPR phenotypes in R

Description

geno.means estimates the founder genotype means and standard errors at a given position.

Usage

geno.means(peakChr, peakPos, model, design, phenotype.dat, id.col, sex)

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).
model	an object of class formula: a symbolic description of the null model to be fitted at each position (e.g., phenotype ~ 1). The genotype effects to be fitted will be added based on design.
design	a character string. One of either 'inbredA', 'inbredB', or 'ABcross' corresponding to the pA and pB set of inbred RILs or the pA-pB cross design. For round robin designs or other cross designs, use the more flexible DSPRgenos and standard model fitting functions in R.
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.
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.
sex	a character string (either 'm' or 'f') specifying the sex of the measured individuals. This argument must be supplied for a cross design for correct specification of the genotypes on the X chromosome.

Value

A data.frame of the estimated mean and standard error for each founder genotype. If a covariate is included in the model statement, the estimate will be the founder genotype mean after correcting for the covariate. If using the ABcross design, a list of data.frames for pA and pB are returned.

Author(s)

Elizabeth King ([e-mail])

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