T1D Application

In this vignette, we walk through an example to illustrate how the fcfdr R package can be used to leverage various relevant genetic and genomic data with GWAS p-values for type 1 diabetes (T1D) to find new genetic associations. This vignette will take approximately 30 minutes to complete.

The data required for this example is available to download within the fcfdr R package and includes:

GWAS p-values for T1D (Onengut-Gumuscu et al. 2015) downloaded from the NHGRI-EBI GWAS Catalog (study GCST005536 accessed on 08/10/21).
GWAS p-values for rheumatoid arthritis (RA) (Eyre et al. 2012) downloaded from the NHGRI-EBI GWAS Catalog (study GCST90013445 accessed on 08/10/21).
Binary measure of SNP overlap with regulatory factor binding sites, derived from merging all DNaseI digital genomic footprinting (DGF) regions from the narrow-peak classifications across 57 cell types (see https://www.nature.com/articles/nature11247). SNP annotations were downloaded for all 1000 Genomes phase 3 SNPs from the LDSC data repository and the binary DGF_ENCODE annotation was extracted for all SNPs in our analysis.
Average fold-enrichment ratios of H3K27ac ChIP-seq counts relative to expected background counts in T1D-relevant cell types. Fold-enrichment ratios were downloaded from NIH Roadmap for CD3, CD4+ CD25int CD127+ Tmem, CD4+ CD25+ CD127- Treg, CD4+ CD25- Th, CD4+ CD25- CD45RA+, CD4 memory, CD4 naive, CD8 memory and CD8 naive primary cells (from https://egg2.wustl.edu/roadmap/data/byFileType/signal/consolidated/macs2signal/foldChange/ see epigenome ID to cell type conversion table here). The fold-enrichment ratios were averaged over cell types to derive the values in column H3K27ac.

Firstly, we download the data:

set.seed(1)
library(fcfdr)
library(cowplot)
library(ggplot2)
library(dplyr)
#> 
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#> 
#>     filter, lag
#> The following objects are masked from 'package:base':
#> 
#>     intersect, setdiff, setequal, union

data(T1D_application_data, package = "fcfdr")
head(T1D_application_data)
#>          rsID CHR19    BP19    REF    ALT   T1D_pval       MAF LDAK_weight
#>        <char> <int>   <int> <char> <char>      <num>     <num>       <num>
#> 1: rs61733845     1 1118275      C      T 0.10475578 0.0353535    0.896405
#> 2:  rs9729550     1 1135242      A      C 0.06329083 0.2575760    0.424584
#> 3:  rs6603788     1 1218086      C      T 0.12616240 0.0656566    0.497992
#> 4:  rs1240708     1 1335790      A      G 0.24334501 0.1464650    0.712747
#> 5:   rs880051     1 1493727      C      T 0.29581294 0.2121210          NA
#> 6:  rs2296716     1 1497824      G      A 0.49740945 0.1161620          NA
#>    RA_pval   DGF   H3K27ac
#>      <num> <int>     <num>
#> 1:  0.3552     0 0.1235078
#> 2:  0.1089     0 2.0741089
#> 3:  0.3700     1 0.1636556
#> 4:  0.6963     0 8.5169011
#> 5:  0.5926     0 0.7284344
#> 6:  0.3080     0 0.5411567

In this application we leverage GWAS p-values for RA, binary SNP overlap with regulatory factor binding sites and H3K27ac counts in T1D-relevant cell types with GWAS p-values for T1D to generate adjusted p-values (called v-values).

orig_p <- T1D_application_data$T1D_pval
chr <- T1D_application_data$CHR19
MAF <- T1D_application_data$MAF
q1 <- T1D_application_data$RA_pval
q2 <- T1D_application_data$DGF
q3 <- log(T1D_application_data$H3K27ac+1) # deal with long tail

The data frame also contains a column of LDAK weights for each SNP (https://dougspeed.com/calculate-weightings/). An LDAK weight of zero means that the signal is (almost) perfectly captured by neighbouring SNPs, and so we use the subset of SNPs with non-zero LDAK weights as our independent subset of SNPs.

ind_snps <- which(T1D_application_data$LDAK_weight != 0)

We are now ready to use the fcfdr R package to generate v-values. Firstly, we generate v-values by leveraging GWAS p-values for RA. We supply MAF values to prevent a bias of the KDE fit towards the behaviour of rarer SNPs (the function intrinsically down-samples the independent subset of SNPs to match the MAF distribution in this subset to that in the whole set of SNPs).

iter1_res <- flexible_cfdr(p = orig_p, 
                           q = q1, 
                           indep_index = ind_snps,
                           maf = MAF)


v1 <- iter1_res[[1]]$v

Since the outputted v-values are analogous to p-values, they can be used directly in any error-rate controlling procedure. Here, we use the Benjamini-Hochberg (BH) procedure to derive FDR-adjusted v-values and plot the resultant FDR values.

res1 <- data.frame(p = orig_p, q1, v1)
mid1 <- median(res1$q1)

ggplot(res1, aes(x = p.adjust(p, method = "BH"), y = p.adjust(v1, method = "BH"), col = q1)) + geom_point(cex = 0.5) + theme_cowplot(12) + background_grid(major = "xy", minor = "none") + geom_abline(intercept = 0, slope = 1,  linetype="dashed") + xlab("Original FDR") + ylab("V1 (FDR)") + ggtitle(paste0("Iteration 1")) + scale_color_gradient2(midpoint = mid1, low = "blue", mid = "white", high = "red", space = "Lab")

The resultant v-values for this first iteration (v1) are then used in the next iteration to leverage binary data on SNP overlap with regulatory factor binding sites. Note that the binary cFDR function implements a leave-one-out procedure and therefore requires a group index for each SNP. This will generally be the chromosome on which that SNP resides but can also be indices relating to LD blocks, for example.

iter2_res <- binary_cfdr(p = v1,
                         q = q2,
                         group = chr)

v2 <- iter2_res$v

res2 <- data.frame(p = v1, v2, q2)
res2$q2 <- as.factor(res2$q2)

ggplot(res2, aes(x = p.adjust(p, method = "BH"), y = p.adjust(v2, method = "BH"), col = q2)) + geom_point(cex = 0.5) + theme_cowplot(12) + background_grid(major = "xy", minor = "none") + geom_abline(intercept = 0, slope = 1,  linetype="dashed") + xlab("V1 (FDR)") + ylab("V2 (FDR)") + ggtitle(paste0("Iteration 2")) + scale_colour_manual(values = c("grey", "black"))

The resultant v-values for this second iteration (v2) are then used in the next iteration to leverage H3K27ac counts.

iter3_res <- flexible_cfdr(p = v2, 
                           q = q3, 
                           indep_index = ind_snps,
                           maf = MAF)

v3 <- iter3_res[[1]]$v

res3 <- data.frame(p = v2, q3, v3)

ggplot(res3, aes(x = p.adjust(p, method = "BH"), y = p.adjust(v3, method = "BH"), col = q3)) + geom_point(cex = 0.5) + theme_cowplot(12) + background_grid(major = "xy", minor = "none") + geom_abline(intercept = 0, slope = 1,  linetype="dashed") + xlab("V2 (FDR)") + ylab("V3 (FDR)") + ggtitle(paste0("Iteration 3")) + scale_color_gradient2(midpoint = 1, low = "blue", mid = "white", high = "red", space = "Lab")

We then create a final data frame containing the results from our analysis. Note that the sign is flipped for q2 and q3. This is because these are negatively correlated with p and the flexible cFDR software automatically flips the sign of q to ensure that low p are enriched for low q.

res <- data.frame(orig_p, q1 = iter1_res[[1]]$q, q2 = as.factor(iter2_res$q), q3 = iter3_res[[1]]$q, v1, v2, v3)

head(res)
#>       orig_p     q1 q2         q3         v1         v2         v3
#> 1 0.10475578 0.3552  0 -0.1164557 0.11041697 0.11826617 0.14932460
#> 2 0.06329083 0.1089  0 -1.1230151 0.04303016 0.04697244 0.02506604
#> 3 0.12616240 0.3700  1 -0.1515664 0.13365968 0.10911264 0.13941567
#> 4 0.24334501 0.6963  0 -2.2530693 0.29820649 0.31427711 0.21649184
#> 5 0.29581294 0.5926  0 -0.5472161 0.34568571 0.36509249 0.34641533
#> 6 0.49740945 0.3080  0 -0.4325332 0.48752645 0.51798495 0.55052819

We can plot the original p-values for T1D against the final adjusted v-values.

mid1 <- median(res$q1)

ggplot(res, aes(x = p.adjust(orig_p, method = "BH"), y = p.adjust(v3, method = "BH"))) + geom_point(cex = 0.5, alpha = 0.5) + theme_cowplot(12) + background_grid(major = "xy", minor = "none") + geom_abline(intercept = 0, slope = 1,  linetype="dashed", col = "red") + xlab("Original P (FDR)") + ylab("V3 (FDR)") + ggtitle(paste0("FDR adjusted v-values\nagainst original FDR values"))

ggplot(res, aes(x = -log10(orig_p), y = -log10(v3))) + geom_point(cex = 0.5, alpha = 0.5) + theme_cowplot(12) + background_grid(major = "xy", minor = "none") + geom_abline(intercept = 0, slope = 1,  linetype="dashed", col = "red") + xlab("Original P (FDR) (-log10)") + ylab("V3 (FDR) (-log10)") + ggtitle(paste0("FDR adjusted v-values against\noriginal FDR values (FDR)")) + coord_cartesian(ylim = c(0,10), xlim = c(0,10))

We find that our implementation of cFDR identifies newly FDR significant SNPs that have relatively small GWAS p-values for rheumatoid arthritis, are more likely to be found in genomic regions where regulatory factors bind and have relatively high H3K27ac counts in T1D relevant cell types.

p_fdr <- p.adjust(orig_p, method = "BH")
v3_fdr <- p.adjust(v3, method = "BH")

# choose fdr threshold corresponding to genome-wide significance threshold
fdr_thr <- max(p_fdr[which(orig_p <= 5*10^{-8})])

median(T1D_application_data$RA_p[which(v3_fdr < fdr_thr & p_fdr > fdr_thr)])
#> [1] 0.0012585
median(T1D_application_data$RA_p)
#> [1] 0.4222

mean(T1D_application_data$DGF[which(v3_fdr < fdr_thr & p_fdr > fdr_thr)])
#> [1] 0.323741
mean(T1D_application_data$DGF)
#> [1] 0.2339995

median(T1D_application_data$H3K27ac[which(v3_fdr < fdr_thr & p_fdr > fdr_thr)])
#> [1] 1.024923
median(T1D_application_data$H3K27ac)
#> [1] 0.5759056

Side comment: code to create the Manhattan plot in the manuscript:

T1D_application_data$v3_fdr <- v3_fdr

nCHR <- length(unique(T1D_application_data$CHR19))
T1D_application_data$BPcum <- NA
s <- 0
nbp <- c()
T1D_application_data <- data.frame(T1D_application_data)
for (i in unique(T1D_application_data$CHR19)){
  nbp[i] <- max(T1D_application_data[T1D_application_data$CHR19 == i,]$BP19)
  T1D_application_data[T1D_application_data$CHR19 == i,"BPcum"] <- T1D_application_data[T1D_application_data$CHR19 == i,"BP19"] + s
  s <- s + nbp[i]
}

axis.set <- T1D_application_data %>% 
  group_by(CHR19) %>% 
  summarize(center = (max(BPcum) + min(BPcum)) / 2)

ggplot(T1D_application_data, aes(x = BPcum, y = -log10(v3_fdr), col = as.factor(CHR19))) + geom_point(cex = 0.75) + theme_cowplot(12) + background_grid(major = "xy", minor = "none") + geom_hline(yintercept = -log10(fdr_thr), linetype = "dashed") + xlab("Position") +  scale_color_manual(values = rep(c("#276FBF", "#183059"), nCHR)) +
  scale_x_continuous(label = axis.set$CHR19, breaks = axis.set$center) + theme(legend.position = "none")+ theme(axis.text.x = element_text(size = 6, angle = 0)) + coord_cartesian(ylim=c(0,10)) + ylab(expression(paste("-log"[10],"(FDR)")))