###########################################################################
# RGenePos #######
# Example Wheat leaf rust from #######
# Based on paper Wamishe et al. 2004 #######
# Version update 21mar16 #######
###########################################################################
## set working directory
setwd("/Users/case0197/Documents/GenePos/example data")
##########################################################################
# load example data from Wamishe et al. 2004 ######
##########################################################################
## this is the data file for unknowns to postulate
lines_IT<-read.csv("lines_IT.csv", head=T, row.names=1)
## this is the data file for single gene differentials
isolines_IT<-read.csv("isolines_IT.csv", head=T, row.names=1)
##########################################################################
# convert raw IT calls ###
# using the SrIT.Convert functoin to convert IT calls to high "H" and ###
# low "L" calls basedon the the cutoff value "33" is minimum "L" value ###
# in this example ###
##########################################################################
## convert the unknowns
lines_HL<-SrIT.Convert(lines_IT, "33")
## convert the differentials
isolines_HL<-SrIT.Convert(isolines_IT, "33")
##########################################################################
# postulate genes ###
# using the GenePos function posulate which resistance genes the ###
# the unknowns might carry. Where "1" is the first unknown in the data ###
# frame of unknowns. Alternatively one may call the unknown by name if ###
# line.name=T is used.
##########################################################################
## postulate the first unknown
GenePos(1, lines_HL, isolines_HL, isolines_IT, lines_IT )
## postulate the second unknown
GenePos(2, lines_HL, isolines_HL, isolines_IT, lines_IT )
## the name of the unknow may also be used
GenePos("MADISON", lines_HL, isolines_HL, isolines_IT, lines_IT, line.name=TRUE)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.