Cross prediction is a method for calculating polygenic scores in large cohorts without the use of summary statistics. For details, refer to this paper.

Note: In the earlier version of the paper (prior to July, 2018), two methods of cross-prediction are proposed: Method 1 and Method 2. In the newer version, Method 1 is referred to as Stack and validate, while Method 2 is referred to as Split-validation. I recommend using Split-validation (Method 2) where possible.

If lassosum is not yet installed, refer to the instruction here for installation. lassosum v0.4.0 or above is required.

Install crosspred using devtools (Note: Windows users need to have installed Rtools.):

# install.packages("devtools") # If devtools not yet installed. 
devtools::install_github("tshmak/crosspred")

Some functions in crosspred use Plink to calculate summary statistics. Before these functions can be used, the link to the plink executable needs to be specified by:

options(lassosum.plink='/path/to/plink')

We assume that we have genotype in PLINK 1 format. For example, let's say our data files are: mydata.bed, mydata.bim, and mydata.fam.

We illustrate crosspred using the toy example PLINK dataset that comes with the lassosum package:

library(lassosum) 
setwd(system.file("data", package="lassosum"))
random.pheno <- rnorm(nrow.bfile("testsample")) # A random phenotype
pl <- cp.plink.linear("testsample", pheno=random.pheno, nfold=2) 
  # This generates the cp.plink.linear object to be used for cross-prediction.
# plot(pl$cor[[1]], pl$cor[[2]]) # The correlation statistics for the two folds can be obtained thus. 

The default is 5-fold cross-prediction. The folds are randomly assigned to the samples. Use nfolds to specify the number of folds needed, or fold to allocate the fold yourself. Type help(cp.plink.linear) for more details.

sumstats can then be fed into cp.lassosum.

ldblocks <- data.table::fread("Berisa.EUR.hg19.bed")
cp <- cp.lassosum(pl, LDblocks = ldblocks)
# plot(cp$pheno, cp$best.pgs) # This is the best PGS using Method 1 (Stack and validate)
# plot(cp$pheno, cp$best.pgs.m2) # This is the best PGS using Method 2 (Split-validation)

We recommend you use one of the LD blocks given in lassosum, if you do not have your own LD blocks defined. These LD blocks are given by the paper Berisa and Pickrell (2015), and are based on the 1000 Genome data. Replace EUR with ASN or AFR for Asian or African LD regions, respectively. hg38 coordinates are also available by liftOver. Simply replace hg19 with hg38 above.

By default, if the sample size is > 5000, cp.lassosum uses a random subset of 5000 as the reference panel. This is to reduce the computation burden. Increase or decrease this using the max.ref.bfile.n option. Alternatively, specify the exact sample to use using the keep.ref option.

For further options, please see the manual

help(cp.lassosum)

or email me at [email protected].

Both cp.plink.linear and cp.lassosum can be run much quicker by multi-threading. For cp.plink.linear, multi-threading is performed by PLINK. For this to work, we need the experimental PLINK 2. For cp.lassosum, we can specify the cluster option.

In large datasets, data is often stored across chromosomes in separate .bed files. To run cross prediction across different chromosomes, simply run cp.plink.linear separately for the different .bed files, then run cp.lassosum separately for each output from cp.plink.linear, specifying list.of.lpipe.output=TRUE. This will generate a list of lassosum.pipeline objects for each fold. However, remember to set the random number seed to the same number before you run cp.plink.linear so that the folds are defined consistently, and also before cp.lassosum if your sample size is > max.ref.bfile.n, so that the same reference sample is chosen! Then, use organize.by.fold to reorganize the all the outputs for the different chromosomes. Finally, run cp.lassosum with the list.of.lpipe.input option. Below is an example for two chromosomes.

set.seed(42)
sumstats1 <- cp.plink.linear("chr1")
set.seed(42)
sumstats2 <- cp.plink.linear("chr2")
set.seed(1000)
lp1 <- cp.lassosum(sumstats1, LDblocks=ld, list.of.lpipe.output=TRUE)
set.seed(1000)
lp2 <- cp.lassosum(sumstats2, LDblocks=ld, list.of.lpipe.output=TRUE)
lp <- organize.by.fold(list(lp1, lp2))
cp <- cp.lassosum(list.of.lpipe.input=lp)

Method 1 in cross-prediction essentially identifies the best lambda and s for use with lassosum. We can then apply this to the entire dataset. This is the cross-validation procedure in our paper, which can be achieved by running:

cv <- cp.cv(sumstats, cp)

sumstats can be a list of cp.plink.linear objects if they were obtained separately for different chromosomes. Note that the order of the list should match that given to cp.lassosum earlier. Note that cp.cv does not calculate summary statistics afresh using the entire data, but simply averages those obtained across the different folds in cp.lassosum. This makes it very fast.

Suppose external summary statistics are loaded into a data.frame called dat with the columns chr, pos, alt, rsid, beta, p for chromosomes, position, alternative allele, rsID, beta coefficients, and p-values respectively. We first need to convert the p-values to correlation coefficients using the p2cor command:

dat$cor <- p2cor(dat$p, n = 60000, sign=dat$beta)

where n = 60000 is the sample size. Assuming cp.pl is an object from cp.plink.linear, we can then run

merged <- cp.meta(cp.pl, chr=chr, pos=pos, snp=rsid, A1=alt, cor=cor, n=60000)

to merge it with cp.pl. We can then proceed with merged as if it were a cp.plink.linear object in running, e.g.,

cp <- cp.lassosum(merged, LDblocks=ld)

Note that not all of the variables chr, pos, snp, A1, A2 need to be specified. At least one of A1 and A2 must be specified. Otherwise specify as many of chr, pos, and snp as you need.

There is an equivalent function cp.pthresh for running cross-prediction using clumping and p-value thresholding instead of lassosum. Refer to the documentation for details.

Please email me [email protected] for any bug reports, comments, or suggestions. Thanks for using crosspred!