In adamwaring/ClusterBurden: Rare variant association utilising burden and positional information.

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.width=7
)

BIN-test no coverage control

1. Generate GnomAD exomes 'controls'
2. Generate GnomAD genomes 'cases'
3. Switch affection status to GnomAD genomes 'cases' to 1 (aff=1)
4. Remove switch to turn on automatic coverage
5. Calculate BIN-test p-values with no coverage control

library(ClusterBurden)

controls = collect_gnomad_controls(dataset="exome", filtertype = "popmax")
cases = collect_gnomad_controls(dataset="genome", filtertype = "popmax")
cases[,aff:=1]

attributes(controls)$provenance = attributes(cases)$provenance = NULL

binpval = BIN_test_WES(cases, controls)

head(binpval)

Proportion of significant results

# nominal significance 
binpval[,sum(BIN.test_pvalue < 0.05, na.rm=T)/.N]

# Bonferonni significance 
binpval[,sum(BIN.test_pvalue < 0.05/.N)/.N]

Lambda (inflation)

# function to generate lambda inflation metric
lambda = function(p) median(qchisq(p, df=1, lower.tail=FALSE)) / qchisq(0.5, 1)

# lambda across all non-NA p-values
lambda(binpval[!is.na(BIN.test_pvalue), BIN.test_pvalue])

# lambda across p-values not in giant proteins i.e. > 2000 residues
lambda(binpval[!is.na(BIN.test_pvalue) & !grepl("high", pl_flag), BIN.test_pvalue])

Manhattan plot

manhattan(binpval, "bin-test", 10, SCALE=0.5)

BIN-test with coverage control

1. Turn back on the switch for automatic coverage control
2. Calculate BIN-test p-values with automatic coverage control

attributes(controls)$provenance = attributes(cases)$provenance = "auto"

binpval = BIN_test_WES(cases, controls)

binpval

Significant results

It is clear that coverage differences was the main driver of significant results. Lambda is now reduced to become below 1 however nominally significant results do exceed 5%. The manhattan plot reveals some Bonferonni significant results indicating either some uncontrolled for confounders (e.g. ancestry) or true differences between the exomes and genomes cohorts (unlikely but not impossible).

# nominal significance 
binpval[,sum(BIN.test_pvalue < 0.05, na.rm=T)/.N]

# Bonferonni significance 
binpval[,sum(BIN.test_pvalue < 0.05/.N, na.rm=T)/.N]

# function to generate lambda inflation metric
lambda = function(p) median(qchisq(p, df=1, lower.tail=FALSE)) / qchisq(0.5, 1)

# lambda across all non-NA p-values
lambda(binpval[!is.na(BIN.test_pvalue), BIN.test_pvalue])

# manhattan
manhattan(binpval, "bin-test", 10, SCALE=0.5)

Alongside the p-values there are flags to alert the user to potential confounders including pl_flag for protein length and cov_flag1 and cov_flag2 for coverage. After removing genes with coverage concern level flagged as high (or very high) the same calculations are made.

binpval = binpval[!grepl("high", cov_flag1) & !grepl("high", cov_flag2) & !grepl("high", pl_flag)]

# nominal significance 
binpval[,sum(BIN.test_pvalue < 0.05, na.rm=T)/.N]

# Bonferonni significance 
binpval[,sum(BIN.test_pvalue < 0.05/.N, na.rm=T)/.N]

# function to generate lambda inflation metric
lambda = function(p) median(qchisq(p, df=1, lower.tail=FALSE)) / qchisq(0.5, 1)

# lambda across all non-NA p-values
lambda(binpval[!is.na(BIN.test_pvalue), BIN.test_pvalue])

# manhattan
manhattan(binpval, "bin-test", 10, SCALE=0.5)

adamwaring/ClusterBurden documentation built on July 29, 2020, 9:50 p.m.