fsearch: Map all of the traits in a given cross object with forward...

In AndersenLab/linkagemapping2: Functions for the Mapping of Andersen Lab RIAILs and RILs using qtl2

Description

Map all of the traits in a given cross object with forward search

Usage

fsearch(cross, phenotype = NULL, permutations = 1000, doGPU = FALSE,
  threshold = "FDR", markerset = c("N2xCB4856", "N2xLSJ2", "AF16xHK104",
  "full", NA))

Arguments

cross	A complete cross object with the phenotype data merged
phenotype	A string or vector of strings used in subsetting the phenotype data. For example: "bleomycin" to map only the traits phenotyped in bleomycin or "amsacrine.q90.TOF" for only that specific trait. To get the union of these two sets, enter c("bleomycin", "amsacrine.q90.TOF").
permutations	The number of permutations for the FDR/GWER calculation. Defaults to 1000.
doGPU	Boolean, whether to use the gputools package to speed up, mapping. This can only be set to TRUE on machines with an NVIDEA graphics card with the gputools package installed. Defaults to FALSE.
threshold	Can be set to either FDR for false discovery rate or GWER for genome-wide error rate. Defaults to FDR.
markerset	The set of markers to use for conversion of position to physical position, if set to NA, no conversion will be completed.

Value

The LOD scores for all markers

AndersenLab/linkagemapping2 documentation built on May 3, 2019, 8:32 p.m.