Multivariate_GWAS

Simply clone the github repository and use R scripts as command-line programs (e.g., Rscript RDA_GWAS.R [arguments]), see details below. All bash code below assumes the repository was cloned into root directory; if not, make sure so change ~/Multivariate_GWAS/ to the actual path. Note: all tables must be space-delimited, and can be compressed .gz files. gt=[filename] Genotypes: table of minor allele counts in each sample (rows - loci, columns - samples). The first two columns must be chromosome, position. Header line must be present (chr, pos, sample names). I recommend running the method on gt files for individual chromosomes, to use less memory and to run it in parallel. (see Appendix about how to get this from angsd). covars.e=[filename] Table of NON-GENETIC covariates (e.g. sampling time, age of individual). These will be regressed out of traits. Rows - samples, columns - covariates. First column must be sample names. Header line must be present (sample, names of covariates). May not fully match the genotype table - the script will match them using the sample column. Rows containing NA will be removed. covars.g=[filename] Table of GENETIC covariates (e.g. sequencing batch, read depth, first couple of genetic PCs). These will be regressed out of genotypes. Same format as covars.e. traits=[filename] Table of trait(s). First column must be sample names. There must be at least 2 columns (samples, 1 trait). Header line must be present (sample, names of traits). Just like covars, this table may not fully match the genotype table; rows containing NAs will be removed. gdist=[filename] Matrix of genetic distances between samples listed in the genotype file (e.g. IBS matrix from angsd, see Appendix). Note: there must be no header line or other non-numeric columns. gdist.samples=[filename] Single-column list of sample names exactly corresponding to the genotype AND genetic distances matrix. Could be filenames with leading path and trailing extension (these will be removed) - basically use the same file that was used for -b argument in angsd to obtain IBS matrix and genotypes (see Appendix). hold.out=[filename] File listing sample names to hold out from the whole analysis for subsequent testing of the polygenic score's prediction accuracy. May be omitted.