In shazanfar/DCARS: Differential Correlation across Ranked Samples

Differential Correlation across Ranked Samples

Overview

DCARS is a flexible statistical approach which uses local weighted correlations to build a powerful and robust statistical test to identify significant variation in levels of concordance across a ranking of samples. This has the potential to discover biologically informative relationships between genes across a variable of interest, such as survival outcome. Read more about DCARS in Bioinformatics.

Installation

knitr::opts_chunk$set(echo = TRUE, warning  = FALSE,message = FALSE)
knitr::opts_chunk$set(cache = TRUE)
knitr::opts_chunk$set(fig.height = 7, fig.width = 7)

# Install the development version from GitHub:
# install.packages("devtools")
devtools::install_github("shazanfar/DCARS")

library(DCARS)

Usage

The following example calculates the DCARS test statistic using the skin cutaneous melanoma (SKCM) TCGA dataset, along survival ranking. First it does so for a single gene pair, SKP1 and SKP2, and then EIF3C and EIF5B. Then DCARS selects the top 10 gene pairs after calculating statistics across the STRING network.

data(STRING)
data(SKCM)
SKCM_rank = t(apply(SKCM,1,rank))

# highly significantly DCARS gene pair: SKP1 and SKP2
# calculates p-value based on permutation
DCARS(SKCM_rank,"SKP1","SKP2", plot=TRUE)

# extract only the test statistic
DCARS(SKCM_rank,"SKP1","SKP2", extractTestStatisticOnly = TRUE)
# examine the weighted correlation vector
wcor = DCARS(SKCM_rank,"SKP1","SKP2", extractWcorSequenceOnly = TRUE)
plot(wcor, type = "l", ylim = c(-1,1)); abline(h = 0, lty = 2)

# plot scatterplot split into five groups by survival ranking
plotColouredExpression(SKCM, genepair = c("SKP1","SKP2"), n = 5)

# plot ribbon plot of genes along sample ranking
plotOrderedExpression(SKCM, gene = c("SKP1", "SKP2"), facet = FALSE)


# not significantly DCARS gene pair: EIF3C and EIF5B
# calculates p-value based on permutation
DCARS(SKCM_rank,"EIF3C","EIF5B",plot=TRUE)
# extract only the test statistic
DCARS(SKCM_rank,"EIF3C","EIF5B", extractTestStatisticOnly = TRUE)
# examine the weighted correlation vector
wcor = DCARS(SKCM_rank,"EIF3C", "EIF5B",extractWcorSequenceOnly = TRUE)
plot(wcor, type = "l", ylim = c(-1,1)); abline(h = 0, lty = 2)

# build weight matrix
W = weightMatrix(ncol(SKCM_rank), type = "triangular", span = 0.5, plot = FALSE)

# extract DCARS test statistics
# should take about 30 seconds
SKCM_stats = DCARSacrossNetwork(SKCM_rank,edgelist = STRING,
                                W = W, extractTestStatisticOnly = TRUE,
                                verbose = FALSE)
sort(SKCM_stats,decreasing=TRUE)[1:10]

To calculate p-values associated with these tests quickly, we use permutation tests over a stratified sample of gene pairs

globalCors = apply(STRING, 1, function(x) cor(SKCM_rank[x[1],], SKCM_rank[x[2],]))

# first take a stratified sample of gene pairs
sampleindices = stratifiedSample(abs(globalCors), length = 50)

# set number of permutations, roughly 1000 or so
niter = 1000

# calculate a large number of permutation statistics from these stratified sample pairs
# this should take about 3-4 minutes
permstats = DCARSacrossNetwork(SKCM_rank,
                               edgelist = STRING[sampleindices,],
                               W = W, 
                               niter = niter,
                               weightedConcordanceFunction = weightedPearson_matrix,
                               weightedConcordanceFunctionW = "matrix",
                               verbose = FALSE,
                               extractPermutationTestStatistics = TRUE)

res = estimatePvaluesSpearman(stats = SKCM_stats, 
globalCors = globalCors, permstats = permstats, 
usenperm = TRUE, nperm = 5000, plot = TRUE, verbose = FALSE)

# plot DCARS statistic against estimated (unadjusted) p-value
# note if there are not enough iterations then the top-most may flatten out
plot(SKCM_stats, -log10(res$pval), col = "red", pch = 16)

# highlight FDR adjusted points
pval_FDR = p.adjust(res$pval, method = "BH")
FDR_sig = pval_FDR < 0.3
sum(pval_FDR < 0.3)

points(SKCM_stats[FDR_sig], -log10(res$pval)[FDR_sig], col = "blue", pch = 16, cex = 1.2)

# What are the most significant (FDR < 0.3) edges?
SKCM_signif_edges_FDR = STRING[FDR_sig,]
SKCM_signif_edges_FDR

Thresholding on unadjusted DCARS p-values (P-value < 0.05) to explore an unweighted network

# extract these significant edges
SKCM_signif_edges = STRING[res$pval < 0.05,]

# and graph them as a network
library(igraph)
SKCM_signif_graph = graph.edgelist(SKCM_signif_edges, directed = FALSE)
V(SKCM_signif_graph)$size = 0.01
V(SKCM_signif_graph)$label.cex = 0.6
plot(SKCM_signif_graph)

# plot network with pathway information overlaid
# pathway information downloaded from MSigDB REACTOME pathways
plotNetworkPathway(SKCM_signif_graph)

# extract network communities and plot
cm = walktrap.community(SKCM_signif_graph)
plot(cm, SKCM_signif_graph)
plot(induced_subgraph(SKCM_signif_graph, V(SKCM_signif_graph)[cm$membership==1]))
plot(induced_subgraph(SKCM_signif_graph, V(SKCM_signif_graph)[cm$membership==2]))
plot(induced_subgraph(SKCM_signif_graph, V(SKCM_signif_graph)[cm$membership==3]))
plot(induced_subgraph(SKCM_signif_graph, V(SKCM_signif_graph)[cm$membership==4]))

Treating DCARS statistics as a network edge weight

library(igraph)
SKCM_graph = graph.edgelist(STRING, directed = FALSE)
E(SKCM_graph)$weight = SKCM_stats
E(SKCM_graph)$pvalweight = -log10(res$pval)

# Graph the Ego network associated with SKP1 with 
plotEgoNetwork(hubnode = c("SKP1"), network = SKCM_graph, weight = "weight")

# only display unadjusted P < 0.05 significant pairs
plotEgoNetwork(hubnode = c("SKP1"), network = SKCM_graph, weight = "pvalweight", subset = TRUE, thresh = -log10(0.05))

SKCM_meanStrength = strength(SKCM_graph, weights = E(SKCM_graph)$weight)/degree(SKCM_graph)

topNodes = names(degree(SKCM_graph))[order(SKCM_meanStrength, decreasing = TRUE)[1:20]]

plot(degree(SKCM_graph), SKCM_meanStrength)
text(degree(SKCM_graph)[topNodes], SKCM_meanStrength[topNodes],
     names(degree(SKCM_graph)[topNodes]))

library(ggplot2)
library(ggrepel)
df = data.frame(node = names(degree(SKCM_graph)),
                degree = degree(SKCM_graph), 
                meanStrength = SKCM_meanStrength, 
                topNodes = (names(degree(SKCM_graph)) %in% topNodes))
g = ggplot(df, aes(x = degree, y = meanStrength)) +
  geom_point() + 
  geom_text_repel(data = subset(df,topNodes==TRUE), aes(label = node)) +
  theme_minimal() +
  NULL
g

# this shows that the strongest genes are IMPDH1 and SKP2, these genes have the highest mean edge weights

Further interrogation

Examine the weighted correlation vector for given genepairs. e.g. we observe a positive association between SKP1 and SKP2, which deteriorates along the sample rankings.

# calculate the weighted correlation vectors across the network
SKCM_wcor = t(DCARSacrossNetwork(SKCM_rank,
                               edgelist = STRING,
                               W = W, 
                               verbose = FALSE,
                               extractWcorSequenceOnly = TRUE))
plotWCorLine(SKCM_wcor, gene = "SKP1")

Examine the significant weighted correlations in terms of clustered pathways

SKCM_signif_wcor = t(DCARSacrossNetwork(SKCM_rank,
                                        edgelist = SKCM_signif_edges,
                                        W = W, 
                                        verbose = FALSE,
                                        extractWcorSequenceOnly = TRUE))

plotWcorsClusterPathway(SKCM_signif_wcor,cluster = TRUE, cutk = 6)