coloc.genome: coloc.genome
In clagiamba/moloc: Multiple Traits Co-localization

Description Usage Arguments Value Author(s) Examples

Genome-wide co-localization with three traits

coloc.genome(listData, bed, prefix = "pref", save.SNP.info = FALSE,
  cores = 20, have_alleles = TRUE, bychrpos = TRUE,
  prior_var = "default", priors = c(1e-04, 1e-06, 1e-07), min_nsnps = 50,
  takelog = FALSE, write = TRUE, outfolder = "test", forcePVAL = FALSE)

`listData,`	a list of data frames in this order: gwas, and other QTLs The data frames need to have columns: "SNP" or "CHR", "POS"; "BETA", "SE"; "N", "MAF" (to estimate sdY) if a case control: "Ncases" If eqtl/mqtl: "ProbeID" Optionally, "A1", "A2" if want to match alleles
`bed,`	a data frame with "CHR", "START", "STOP", and "ProbeID" matching either eqtl or mqtl
`prefix,`	character, name to give to the output file
`save.SNP.info,`	logical, should info of each SNP be saved? If this option is true, beware that it will takes up a lot of time and space.
`cores,`	number. See foreach package.
`have_alleles,`	logical. If TRUE, matches alleles to be the same as gwas data.
`bychrpos,`	logical. If TRUE, uses "CHR", "POS" columns as SNP id to match across data frames; If TRUE, make sure not to have another column called "SNP".
`prior_var,`	numeric vector specifying any number of values; These will be used to average the ABF computation across different prior variances.
`priors,`	numeric vectors with three numbers; First number is the prior of associaion of a SNP with any of the traits; Second number is the prior of a SNP being associated with two traits; Third number is the prior of a SNP being associated with three traits.
`min_nsnps,`	number. The minimum number of matching SNPs across the three data frames to consider.
`outfolder,`	path of folder where the results will be written to

results in outfolder: text file with colocalization results for each locus; text file with removed snps; if save.SNP.info = TRUE, a folder called "coloc.output.perSNP" will save a file per locus with SNP information such as ABF (one row per matching SNP)

Claudia Giambartolomei

library(mvtnorm)
library(foreach)
library(doParallel)
library(data.table)

Create bed file with combination of ProbeIDs
library(GenomicRanges)
DT <- as.data.table(data_genome[[3]])
methyl_table <- DT[, list(CHR= unique(CHR), START = min(POS), STOP = max(POS)), by = ProbeID]
bed1.gr <- GRanges(seqnames = bed$CHR,IRanges(start = bed$START, end= bed$STOP))
bed2.gr <- GRanges(seqnames = methyl_table$CHR,IRanges(start =methyl_table$START, end= methyl_table$STOP))
my.overlap <- findOverlaps(query = bed2.gr, subject = bed1.gr)
bed = cbind(bed[my.overlap@subjectHits,], methyl_table[my.overlap@queryHits,])
bed = bed[,c(1,6,7,8,9,10)]
Setting the prior_var to "default" uses coloc defaults
coloc.genome(listData = data_genome, bed, cores=1, have_alleles=TRUE, bychrpos=TRUE, prior_var=NULL, priors=c(1e-04, 1e-06, 1e-07), min_nsnps = 50, write=FALSE, outfolder = "test")