dougspeed.com
REML Analysis | dougspeed.com
http://dougspeed.com/reml-analysis
The only OFFICIAL website of Doug Speed. To which the following options can be added (to restrict to a subset of the data see Data Filtering. 8211; required to provide the responses ( in PLINK format. Individuals without a phenotype will be excluded. If phenofile. Contains more than one phenotype, specify which should be used with –mpheno. Or –mgrm grmlist. 8211; to provide one or more kinship matrices. And use –weights. Or –ignore-weights YES. 8211; to provide covariates ( in PLINK format. 8211; contain...
dougspeed.com
MultiBLUP | dougspeed.com
http://dougspeed.com/multiblup
The only OFFICIAL website of Doug Speed. For constructing linear prediction models, we recommend MultiBLUP, a generalisation of BLUP (Best Linear Unbiased Prediction). Full details of the method are provided in our Genome Research paper. In brief, MultiBLUP extends the BLUP model to allow for k r genetic random effect terms:. And e N(0,Iv. Just like with BLUP, there are two steps when constructing a MultiBLUP prediction model: first you perform REML to estimate the variance terms v. Seems to work best fo...
dougspeed.com
Adjusting for LD | dougspeed.com
http://dougspeed.com/adjusting-for-ld
The only OFFICIAL website of Doug Speed. The original purpose of LDAK was to create kinship matrices adjusted for linkage disequilibrium. The main two steps are:. 1 – calculate weightings which reflect the local patterns of correlations across predictors. 2 – (given these weightings) calculate pairwise kinship estimates across samples. For instructions on the former. For instructions on the latter. When calculating weightings using population GWAS data, we advise keeping the LD decay parameters.
dougspeed.com
Genomic Partitioning | dougspeed.com
http://dougspeed.com/genomic-partitioning
The only OFFICIAL website of Doug Speed. To consider subsets of predictors, use the options. Eg, create index files list1. Then when cutting the genome add –partition-number 3. And –partition-prefix list. When performing genomic partitioning. Consider the following examples using the binary PLINK files test.bed. Testbim and test.fam. In the Test Datasets. In total, there are 5000 predictors. A – we wish to compare h. B – we wish to compare h. C – we wish to compare h. From {1-350}, {300-500} and {2801-50...
dougspeed.com
Adaptive MultiBLUP | dougspeed.com
http://dougspeed.com/adaptive-multiblup
The only OFFICIAL website of Doug Speed. To run (basic) Adaptive MultiBLUP, there are six steps. Step 1: divide the genome into chunks –cut-genes folder. Step 2: test the chunks for association –calc-genes-reml folder. Step 3: create regions based on significant chunks –join-genes-reml folder. Step 4: calculate the background kinship matrix –calc-kins-direct output. Step 5: estimate variance components for the MultiBLUP Model –reml output. Covariates can be included. By adding –covar. As we discuss here.
dougspeed.com
Kinship Manipulation | dougspeed.com
http://dougspeed.com/kinship-manipulation
The only OFFICIAL website of Doug Speed. LDAK can both add and subtract kinship matrices. The latter can be useful for Genomic Paritioning. Suppose that you wish to construct two kinship matrices, one corresponding to a small region and one to the rest of the genome. Rather than calculate both from scratch, you can instead compute the regional kinship matrix, then obtain its complement by subtracting this from the genome-wide kinship matrix. 8211;add-grm output –mgrm kinstems. And save to output. To save...
dougspeed.com
Test Datasets | dougspeed.com
http://dougspeed.com/test-datasets
The only OFFICIAL website of Doug Speed. Test datasets are also available on the main download. All demonstration commands on this site assume you are in the examples. Folder (so once you unzip the ldak file, you will see three folders: source. So most likely, you will have to replace this with the version specific link, such as. Or rename the version specific executable ldak.out. And remember, all arguments are preceded by two dashes, even if on the website this shows up as one long dash!
dougspeed.com
Pre-specified Kinships | dougspeed.com
http://dougspeed.com/pre-specified-kinships
The only OFFICIAL website of Doug Speed. The most basic use of MultiBLUP is when we have already computed a number of kinship matrices (which because the aim is prediction we advise doing with weightings turned off. And wish to perform generalised BLUP. First we estimate the variance components. 8211;reml output –pheno phenofile –mgrm grmlist. Provides the stems of the pre-computed kinship matrices and phenofile. Provides the phenotypic values ( stored in PLINK format. Add the option –covar. Ldakout R...
dougspeed.com
Downloads | dougspeed.com
http://dougspeed.com/downloads
The only OFFICIAL website of Doug Speed. Tuesday 24th March – LDAK.4.9 now available. As LDAK4 contains many new features, I expect there are some bugs I’ve missed (sorry), so please keep an eye here for updated versions. And if you find any errors, please email doug dot speed at ucl dot ac dot uk. First time users, please enter your details and press Send to download LDAK.4.9. Downloaded before, or form not working? The previous versions are still available:. With examples folder here. Gcc -Wl,–al...
dougspeed.com
Get Kinships | dougspeed.com
http://dougspeed.com/get-kinships
The only OFFICIAL website of Doug Speed. In LDAK4, there are two ways to compute kinships. The direct method ( –calc-kins-direct. Are REQUIRED; options in purple. Are OPTIONAL. If you wish to only analyse a subset of the data, see Data Filtering. In all cases, folder. Is the directory in which output will be written. Bfile/ chiamo/ sp/–speed prefix. 8211; specifies the data files ( see File Formats. Else you can provide your own weights file, which should have two columns providing predictor names then w...
