Reference

All functions

Var.data()

helper function to compute shrinkage factor for a quantitative trait

Var.data.cc()

helper function to compute shrinkage factor for a case/control trait

approx.bf.p()

This function computes posterior probabilities for a variant to be causal using Wakefields asymptotic Bayes Factors.

compute_cogs()

This function computes COGS scores for a given trait across a set of pchic regions

csnps.gr

csnps.gr Coding SNPs for chromosome 22.

digest.gr

digest.gr HindIII restriction digest for chromosome 22.

feature.sets

feature.sets Feature sets from Javierre et al pcHi-C dataset for chromosome 22.

fix_chr()

This function fixes chromosomes so they are numeric

ld.gr

ld.gr HapMap approx 1cM LD blocks for chromosome 22.

load_capture_design()

This loads a capture design file with columns fragid and ensg. fragid should match digest file.

load_digest()

This loads a restriction digest file with columns chr,start,end and fragid

load_gwas()

This function loads and checks set of univariate P values for a given trait and adds posterior probabilities for each SNP to be causal using Wakefield's aBF

load_ld_regions()

This function checks and loads and checks a set of non overlapping LD regions expects three column tab delim file with colnames chr,start,end

load_ref_maf()

This function checks and loads a reference set of maf expects three columns tab delim file with colnames chr,pos and maf

logsum()

helper function to sum logs without loss of precision logsum sums logs without loss of precision

maf.DT

maf.DT Reference minor allele frequencies from UK10K for chromosome 22.

make_csnps()

This function loads in a coding SNPs matched to a given ensembl id, columns are chr,pos and ensg

make_pchic()

This function computes loads in a set of promoter capture Hi-C files (pcHi-C). This is a tab delimited file that contains the following mandatory columns

  1. ensg - Ensembl gene id for gene

  2. name - Gene name

  3. biotype - Gene biotype from ensembl e.g. protein_coding

  4. strand - Gene strand

  5. baitChr - Bait (A captured restriction fragment) chromosome

  6. baitStart - Bait fragment start

  7. baitEnd - Bait fragment end

  8. baitID - Bait fragment ID should match ID in digest file

  9. baitName - Free text of what is captured - deprecated.

  10. oeChr - 'Other end' (Promoter interacting restriction fragment) chromosome

  11. oeStart - 'Other end' fragment start

  12. oeEnd - 'Other end' fragment end

  13. oeID - 'Other end' fragment ID should match ID in digest file

  14. oeName - Free text of what is interacting - deprecated.

Additional columns contain CHiCAGO scores for one or more columns.

make_vprom()

This function computes 'Virtual' promoter regions. These are baited fragments and the fragments either side.

t1d.DT

t1d.DT GWAS data from Cooper et al. for Type 1 diabetes for chromosome 22.