####################################################################

          ### BULK SEGREGANT ANALYSIS USING SNP CHIPS ###

#This script launches the function that performs BSA using SNP chips
#with the help of some user input. Before beginning, the user must
#have the following two directories:
# 
# 1. a Supplementary Directory containing:
#       a. BSAsnp.R (i.e this script)
#       b. File_S9_BSAsnp.supplies.txt
#       c. snp.RData
#       d. snp.calls1020.RData
#
# 2. a Files Directory containing the .CEL files to be analyzed
#      *note: this directory is where output will be saved
#
#
# Becker, July 2010
####################################################################




# To start, replace the argument of the source command below with
# the full path to "BSAsnp.supplies.R" on your computer, then
# copy and paste both lines of script to the command line on the
# console and press enter to evaluate.

source("/Users/tonybecker/Desktop/BSA_Supplement/File_S9_BSAsnp.supplies.txt")
BSAsnp()

# Then, follow the instructions on the console.