logistic factor analysis
Pre-print available: http://arxiv.org/abs/1312.2041
Apple OS X users, see FAQ below. To install, open R and type:
install.packages("devtools") library("devtools") install_github("Storeylab/lfa")
read.bed to read in a PLINK binary genotype file, or manually reading a text file of 0, 1, and 2 via
read.table with the
colClasses option set to
rep("integer", n), where
n is the number of individuals.
Be warned that both the
lfa function and the genotype matrices require a lot of memory, since we're just storing the genotype matrices as integer arrays (which take up a lot of space in R!) and doing normal math operations on them. As a rule of thumb, the in memory sizes of a few relevant genotype matrices:
- 431345 SNPs by 940 individuals: 1.5 Gb needed for genotype matrix, about 9 Gb to run
- 339100 SNPs by 1500 individuals: 1.9 Gb needed for genotype matrix, about 11.5 Gb to run
If you want to run something but don't have the computing power for it, shoot me an email at firstname.lastname@example.org. There are number of workarounds that can trade off between memory and time that I've used in the past.
Apple OS X users may experience a problem due to Fortran code that is included in this package. This gfortran issue is discussed here:
A solution that has worked for us is to follow the advice given above. Specifically, open a Terminal and type:
curl -O http://r.research.att.com/libs/gfortran-4.8.2-darwin13.tar.bz2 sudo tar fvxz gfortran-4.8.2-darwin13.tar.bz2 -C /
If you know what causes this, let us know!