## ---- include = FALSE----------------------------------------------------
knitr::opts_chunk$set(collapse = TRUE, comment = "#>")
library(lmem.qtler)
## ---- eval = FALSE-------------------------------------------------------
# library(lmem.qtler)
# data (DHpop_pheno)
# data (DHpop_geno)
# data (DHpop_map)
# G.data <- DHpop_geno
# map.data <- DHpop_map
# P.data <- DHpop_pheno
#
# cross.data <- qtl.cross (P.data, G.data, map.data, cross='dh',
# heterozygotes=FALSE)
# summary (cross.data)
#
# ## Pheno Quality
# pq.diagnostics (crossobj=cross.data)
#
# ## Marker Quality
# mq.diagnostics (crossobj=cross.data,I.threshold=0.1,
# p.val=0.01,na.cutoff=0.1)
#
## ---- eval = FALSE-------------------------------------------------------
# ### QTL_SMA
# QTL.result <- qtl.analysis (crossobj=cross.data,step=0, method='SIM',
# trait="height", threshold="Li&Ji", distance=30,
# cofactors=NULL, window.size=30)
#
# ### QTL_SIM
# QTL.result <- qtl.analysis ( crossobj=cross.data, step=5,
# method='SIM',trait="height", threshold="Li&Ji",
# distance=30,cofactors=NULL, window.size=30)
## ---- eval = FALSE-------------------------------------------------------
# ### QTL CIM
# cofactors <- as.vector (QTL.result$selected$marker)
# QTL.result <- qtl.analysis ( crossobj=cross.data, step=5,
# method='CIM', trait="height", threshold="Li&Ji",
# distance=30, cofactors=cofactors, window.size=30)
#
## ---- eval = FALSE-------------------------------------------------------
# data (SxM_geno)
# data (SxM_map)
# data (SxMxE_pheno)
#
# P.data <- SxMxE_pheno
# G.data <- SxM_geno
# map.data <- SxM_map
#
# cross.data <- qtl.cross (P.data, G.data, map.data, cross='dh',
# heterozygotes=FALSE)
#
# summary (cross.data)
# jittermap(cross.data)
#
# Pheno Quality
# pq.diagnostics (crossobj=cross.data, boxplot=FALSE)
#
# Marker Quality
# mq.diagnostics (crossobj=cross.data,I.threshold=0.1,
# p.val=0.01,na.cutoff=0.1)
#
# ### QTL_SIM
# QTL.result <- qtl.memq (crossobj = cross.data, P.data = P.data,
# env.label = c('ID91','ID92','MAN92','MTd91',
# 'MTd92','MTi91','MTi92','SKs92','WA91','WA92'),
# trait = 'yield', step = 10, method = 'SIM',
# threshold = 'Li&Ji', distance = 50, cofactors = NULL,
# window.size = 50)
#
# ### QTL_CIM
# QTL.result <- qtl.memq (crossobj = cross.data, P.data = P.data,
# env.label = c('ID91','ID92','MAN92','MTd91','MTd92',
# 'MTi91','MTi92','SKs92','WA91','WA92'),
# trait = 'yield', step = 10, method = 'CIM',
# threshold = 'Li&Ji', distance = 50,
# cofactors = QTL.result$selected$marker, window.size = 50)
#
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