SummaryAM: Summary of multiple locus association mapping results

In Eagle: Multiple Locus Association Mapping on a Genome-Wide Scale

Description

A summary function that provides additional information on the significant marker-trait associations found by AM

Usage

SummaryAM(AMobj = NULL, pheno = NULL, geno = NULL, map = NULL)

Arguments

AMobj	the (list) object obtained from running AM. Must be specified.
pheno	the (data frame) object obtained from running ReadPheno. Must be specified.
geno	the (list) object obtained from running ReadMarker. Must be specified.
map	the (data frame) object obtained from running ReadMap. The default is to assume a map object has not been supplied. Optional.

Details

SummaryAM produces two tables of results. First, a table of results is produced with the additive effect size and p-value for each fixed effect in the final model. Second, a table of results is produced with the proportion of phenotypes variance explained by the different multiple-locus models. Each row in this table is the proportion of phenotype variance after the marker locus has been added to the multiple locus model. Our calculations of variance explained are based on Sun et al. (2010).

References

Sun G., Zhu C., Kramer MH., Yang S-S., et al. 2010. Variation explained in mixed model association mapping. Heredity 105, 330-340.

See Also

AM

Examples

 ## 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, availmemGb=8)

  #-----------------------------------------
  # Produce additional summary information 
  #------------------------------------------

  SummaryAM(AMobj=res, pheno=pheno_obj, geno=geno_obj, map=map_obj)
 
## End(Not run)

Eagle documentation built on May 2, 2019, 5:31 p.m.