Eagle can handle data recorded on inbred or outbred individuals.
Eagle is an R package, that makes heavy use of c++.
Organize your input data into three files; a file with the marker data, a file with the phenotypic data, and a file with the map. The marker file has rows which correspond to data on individuals and columns which correspond to data on snp. The phenotype file has rows which correspond to data on individuals and columns which correspond to data on traits and fixed effects. The map file has rows that correspond to snp. Each file is read into Eagle separately.
Eagle will run without a marker map being supplied. Unlike classic linkage mapping, association mapping doesn't require a known marker map. However, for interprability of the results, it is best to also supply a marker map.
Eagle does its best to capture errors, especially in the input files. Eagle also issues error messages that we hope will be helping for solving the problem.
This has been a source of frustration. The file browser has opened, it is sitting in the background. This behaviour of the R file browser opening behind instead of in front of the active window is a known problem which has yet to be solved.
Make sure you are running the latest version of R along with updated versions of the packages (use update.packages
).
Go back to the window from which you issued the OpenGUI
command. If an error has occurred, it will be printed here.
The most likely cause is that your packages have been installed under a version of R that is different to the one being used.
Run the following to update all your installed packages
update.packages(checkBuilt=TRUE, ask=FALSE)
Eagle can deal with two types of marker data; genotypic and allelic. If marker genotypes are available, then they need to be in a plain space separated text file where the rows are the individuals and the columns are the snps. The file should not contain row or column headings. The genotypes can be any alphanumeric value, as long as these same alphanumeric values are used across all the loci. If allelic data are available, then this needs to be in PLINK ped form.
Yes. If genotype data are available, then any alphanumeric value can be used to denote missing data. If allelic data are available, PLINK only allows 0 or - to be missing alleles.
Eagle sets the missing marker genotypes to AB. Since Eagle assumes an additive locus model, setting a missing genotype to AB is equivalent to imputing a genotype that has no effect on a trait. If there are a large number of missing genotypes, this will reduce the power for detecting marker-trait associations. A better strategy is to impute the missing marker genotypes prior to analysis with Eagle with dedicated imputation software such as BEAGLE or fastPHASE.
Yes. Eagle can analyse marker data larger than the memory capacity of a computer by using out-of-memory matrix calculation.
Make sure a line does not begin with a space. Also check that each line has the same number of entries. We've also encountered
problems when transferring files from a windows system to a unix system and vise versa.
This is because the format for a windows and a unix text file differ slightly in how they handle the end of a line. When transferring
files between different platforms, it is good practice to use a file conversion program first, such as dos2unix and unix2dos.
Yes. Suppose you have dominant marker data with genotype codes 0 and 1 for absence and presence, respectively.
Then, when the marker data is being read with Read Genotypes
, set the parameter AA to 0 and BB to 1 (or vise versa) but
leave AB blank. If you have a multi-allelic locus, say with 10 segregating alleles, then turn this locus into 10
dominant loci and treat these loci as described.
Yes. Individuals with missing trait and/or fixed effects are removed from the analysis. However, only individuals whose data are being considered for analysis will be removed. Individuals with missing data not involved in the analysis will not be removed.
Yes.
Yes
Yes. The rows are ordered by individual in the phenotypic file. This same ordering of rows by individual must be followed for the marker file. Eagle will check to make sure the total number of rows in the genotypic and phenotypic files match. However, Eagle cannot check that the ordering of the rows in both files is the same.
If Eagle has not been previously installed, then start R and at the R prompt, type
install.packages("Eagle", dependencies=TRUE)
Eagle is dependent upon several other packages. This command will install Eagle, along with any missing packages upon which Eagle is dependent.
If Eagle is already installed, but you you want the latest version of Eagle, then at the R prompt, type
update.packages(checkBuilt=TRUE, ask=FALSE)
Yes.
We have seen some strange behaviour, especially with OpenGUI()
, when Eagle and its dependencies
have been installed under different versions of R. When ever a newer version of R is installed, it is good practice to
update it's packages with
update.packages(checkBuilt=TRUE, ask=FALSE)
Eagle will run on the same platforms that R will run on which are Linux, OS X (Mac), and Windows.
Yes, but there may be a loss in power for detecting marker-trait associations. Eagle is based on linear mixed models. Linear mixed models assume a response (or trait) is normally distributed. However, they are robust to violations of their assumptions.
Yes, but using Eagle via OpenGUI can only handle main effects. One solution is to add an
extra column to the phenotypic data file that is the interaction of the two effects that are of interest. Then, include these data
as an extra fixed effect in the analysis. Alternately, from the R prompt, use the AM
function and define the fixed effect part of the model
by setting fformula. It would be best to look online for information on how to specify
linear models in R which include interaction terms.
Not all parts of an Eagle analysis is parallelized. However, you should be seeing multiple threads being used at different times throughout each iteration of the model. It is most likely that your version of R is not making use of a multi-threaded BLAS library such as MKL or openBLAS. Look at our installation notes on how to install R that is multi-threaded.
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