Description Usage Arguments Details See Also Examples
A summary function that provides additional information on the significant
marker-trait associations found by AM
1 |
AMobj |
the (list) object obtained from running |
SummaryAM
produces three tables, an overall summary table, a table of the
SNP names and positions, and a table of results with
the p-value for each
fixed effect in the final model.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 | ## Not run:
# Since the following code takes longer than 5 seconds to run, it has been tagged as dontrun.
# However, the code can be run by the user.
#
#---------------
# read the map
#---------------
#
# File is a plain space separated text file with the first row
# the column headings
complete.name <- system.file('extdata', 'map.txt',
package='Eagle')
map_obj <- ReadMap(filename=complete.name)
# to look at the first few rows of the map file
head(map_obj)
#------------------
# read marker data
#------------------
# Reading in a PLINK ped file
# and setting the available memory on the machine for the reading of the data to 8 gigabytes
complete.name <- system.file('extdata', 'geno.ped',
package='Eagle')
geno_obj <- ReadMarker(filename=complete.name, type='PLINK', availmemGb=8)
#----------------------
# read phenotype data
#-----------------------
# Read in a plain text file with data on a single trait and two fixed effects
# The first row of the text file contains the column names y, cov1, and cov2.
complete.name <- system.file('extdata', 'pheno.txt', package='Eagle')
pheno_obj <- ReadPheno(filename=complete.name)
#-------------------------------------------------------
# Perform multiple-locus genome-wide association mapping
#-------------------------------------------------------
res <- AM(trait = 'y',
fformula=c("cov1 + cov2"),
map = map_obj,
pheno = pheno_obj,
geno = geno_obj)
#-----------------------------------------
# Produce additional summary information
#------------------------------------------
SummaryAM(AMobj=res)
## End(Not run)
|
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