SNPassoc: an R package to perform whole genome association studies
2020-09-07
Package
SNPassoc 2.0.0
1 Introduction
The SNPassoc package contains facilities for data manipulation, tools for exploratory data analysis, convenient graphical facilities, and tools for assessing genetic association for both quantitative and categorial (case-control) traits in whole genome approaches. Genome-based studies are normally analyzed using a multistage approach. In the first step researchers are interested in assessing association between the outcome and thousands of SNPs. In a second and possibly third step, medium/large scale studies are performed in which only a few hundred of SNPs, those with a putative association found in the first step, are genotyped. SNPassoc is specially designed for analyzing this kind of designs. In addition, a convenience-based approach (select variants on the basis of logistical considerations such as the ease and cost of genotyping) can also be analyzed using SNPassoc. Different genetic models are
also implemented in the package. Analysis of multiple SNPs can be analyzed using either haplotype or gene-gene interaction approaches.
This document is an updated version of the initial vignette that was published with the SNPassoc paper González et al. (2007). It contains a more realistic example belonging to a real dataset. The original vignette is still available here.
2 Data loading
SNP data are typically available in text format or Excel spreadsheets which are easily uploaded in R as a data frame. Here, as an illustrative example, we are analyzing a dataset containing epidemiological information and 51 SNPs from a case-control study on asthma. The data is available within SNPassoc and can be loaded by
Then, the data is loaded into the R session by
data(asthma, package = "SNPassoc")
str(asthma, list.len=9)'data.frame': 1578 obs. of 57 variables:
$ country : Factor w/ 10 levels "Australia","Belgium",..: 5 5 5 5 5 5 5 5 5 5 ...
$ gender : Factor w/ 2 levels "Females","Males": 2 2 2 1 1 1 1 2 1 1 ...
$ age : num 42.8 50.2 46.7 47.9 48.4 ...
$ bmi : num 20.1 24.7 27.7 33.3 25.2 ...
$ smoke : int 1 0 0 0 0 1 0 0 0 0 ...
$ casecontrol: int 0 0 0 0 1 0 0 0 0 0 ...
$ rs4490198 : Factor w/ 3 levels "AA","AG","GG": 3 3 3 2 2 2 3 2 2 2 ...
$ rs4849332 : Factor w/ 3 levels "GG","GT","TT": 3 2 3 2 1 2 3 3 2 1 ...
$ rs1367179 : Factor w/ 3 levels "CC","GC","GG": 2 2 2 3 3 3 2 3 3 3 ...
[list output truncated]asthma[1:5, 1:8] country gender age bmi smoke casecontrol rs4490198 rs4849332
1 Germany Males 42.80630 20.14797 1 0 GG TT
2 Germany Males 50.22861 24.69136 0 0 GG GT
3 Germany Males 46.68857 27.73230 0 0 GG TT
4 Germany Females 47.86311 33.33187 0 0 AG GT
5 Germany Females 48.44079 25.23634 0 1 AG GGWe observe that we have case-control status (0: control, 1: asthma) and another 4 variables encoding the country of origin, gender, age, body mass index (bmi) and smoking status (0: no smoker, 1: ex-smoker, 2: current smoker). There are 51 SNPs whose genotypes are given by the alleles names.
3 Descriptive analysis
To start the analysis, we must indicate which columns of the dataset asthma contain the SNP data, using the setupSNP function. In our example, SNPs start from column 7 onwards, which we specify in argument colSNPs
library(SNPassoc)
asthma.s <- setupSNP(data=asthma, colSNPs=7:ncol(asthma), sep="")This is an alternative way of determining the columns containing the SNPs
idx <- grep("^rs", colnames(asthma))
asthma.s <- setupSNP(data=asthma, colSNPs=idx, sep="")The argument sep indicates the character separating the alleles. The default value is ’‘/´´. In our case, there is no separating character, so that, we set sep="". The argument name.genotypes can be used when genotypes are available in other formats, such as 0, 1, 2 or’‘norm´´,’‘het´´,’’mut´´. The purpose of the setupSNP function is to assign the class snp to the SNPs variables, to which SNPassoc methods will be applied. The function labels the most common genotype across subjects as the reference one. When numerous SNPs are available, the function can be parallelized through the argument mc.cores that indicates the number of processors to be used. We can verify that the SNP variables are given the new class snp
head(asthma.s$rs1422993)[1] G/G G/T G/G G/T G/T G/G
Genotypes: G/G G/T T/T
Alleles: G T class(asthma.s$rs1422993)[1] "snp" "factor"and summarize their content with summary
summary(asthma.s$rs1422993)Genotypes:
frequency percentage
G/G 903 57.224335
G/T 570 36.121673
T/T 105 6.653992
Alleles:
frequency percentage
G 2376 75.28517
T 780 24.71483
HWE (p value): 0.250093 which shows the genotype and allele frequencies for a given SNP, testing for Hardy-Weinberg equilibrium (HWE). We can also visualize the results in a plot by
plot(asthma.s$rs1422993)
Figure 1: SNP summary
Bar chart showing the basic information of a given SNP
The argument type helps to get a pie chart
plot(asthma.s$rs1422993, type=pie)
Figure 2: SNP summary
Pie chart showing the basic information of a given SNP
The summary function can also be applied to the whole dataset
summary(asthma.s, print=FALSE) alleles major.allele.freq HWE missing (%)
rs4490198 A/G 59.2 0.174133 0.6
rs4849332 G/T 61.8 0.522060 0.1
rs1367179 G/C 81.4 0.738153 1.0
rs11123242 C/T 81.7 0.932898 0.6
rs13014858 G/A 58.3 0.351116 0.1
rs1430094 G/A 66.9 0.305509 0.4
rs1430093 C/A 66.6 0.817701 3.5
rs746710 G/C 51.5 0.614368 0.0
rs1430090 T/G 70.0 0.025180 1.6
rs6737251 C/T 69.3 0.235996 0.3
rs11685217 C/T 80.1 0.009462 4.5
rs1430097 C/A 65.1 0.738166 1.0
rs10496465 A/G 85.8 0.917997 0.6
rs3756688 T/C 63.9 0.154632 0.6
rs2303063 A/G 53.0 0.722069 1.1
rs1422993 G/T 75.3 0.250093 0.0
rs2400478 G/A 62.6 0.256786 0.9
rs714588 A/G 54.9 0.838329 0.8
rs1023555 T/A 76.8 0.943443 0.5
rs898070 G/A 62.6 1.000000 0.6
rs963218 C/T 53.2 0.389387 0.3
rs1419835 C/T 78.2 0.505391 0.6
rs765023 T/C 64.5 0.030513 6.9
rs1345267 A/G 61.0 0.112183 0.1
rs324381 G/A 64.6 0.242223 11.6
rs184448 T/G 55.9 0.008446 2.2
rs324396 C/T 71.2 0.197291 0.3
rs324957 G/A 57.0 0.007417 0.4
rs324960 C/T 66.6 0.077777 1.1
rs10486657 C/T 81.3 0.672703 4.3
rs324981 A/T 53.2 0.048438 0.2
rs1419780 C/G 80.8 0.569652 0.2
rs325462 T/A 51.0 0.337862 0.3
rs727162 G/C 78.5 0.765708 0.0
rs10250709 G/A 65.4 0.266434 0.0
rs6958905 T/C 64.7 0.377472 0.4
rs10238983 T/C 75.7 0.216435 0.4
rs4941643 A/G 54.1 0.635887 7.2
rs3794381 C/G 71.7 0.652089 7.1
rs2031532 G/A 65.0 0.911918 0.0
rs2247119 T/C 71.5 0.457710 0.5
rs8000149 T/C 63.2 0.588077 0.4
rs2274276 G/C 57.0 0.571386 0.6
rs7332573 G/T 91.5 0.869947 1.5
rs3829366 T/A 51.6 0.722626 1.3
rs6084432 G/A 83.7 0.266716 0.6
rs512625 G/A 69.5 0.905395 0.4
rs3918395 G/T 86.8 0.508732 1.2
rs2787095 G/C 60.2 0.102053 0.8
rs2853215 G/A 73.0 0.249516 0.2 showing the SNP labels with minor/major allele format, the major allele frequency the HWE test and the percentage of missing genotypes. Missing values can be further explored plotting with
plotMissing(asthma.s, print.labels.SNPs = FALSE)
Figure 3: Missing genotypes
Black squares shows missing genotuype information of asthma data example.
This plot can be used to inspect if missing values appear randomly across individuals and SNPs. In our case, we can see that the missing pattern may be considered random, except for three clusters in consecutive SNPs (large black squares). These individuals should be further checked for possible problems with genotyping.
4 Hardy-Weinberg equilibrium
Genotyping of SNPs needs to pass quality control measures. Aside from technical details that need to be considered for filtering SNPs with low quality, genotype calling error can be detected by a HWE test. The test compares the observed genotype frequencies with those expected under random mating, which follows when the SNPs are in the absence of selection, mutation, genetic drift, or other forces. Therefore, HWE must be checked only in controls. There are several tests described in the literature to verify HWE. In SNPassoc HWE is tested for all the bi-allelic SNP markers using a fast exact test Wigginton, Cutler, and Abecasis (2005) implemented in the tableHWE function.
hwe <- tableHWE(asthma.s)
head(hwe) HWE (p value)
rs4490198 0.1741325
rs4849332 0.5220596
rs1367179 0.7381531
rs11123242 0.9328981
rs13014858 0.3511162
rs1430094 0.3055089We observe that the first SNPs in the dataset are under HWE since their P-values rejecting the HWE hypothesis (null hypothesis) are larger than 0.05. However, when tested in control samples only, by stratifying by cases and controls
hwe2 <- tableHWE(asthma.s, casecontrol)
#SNPs is HWE in the whole sample but not controls
snpNHWE <- hwe2[,1]>0.05 & hwe2[,2]<0.05
rownames(hwe2)[snpNHWE][1] "rs1345267"hwe2[snpNHWE,]all groups 0 1
0.11218285 0.04956349 0.81604706 We see that rs1345267 is not in HWE within controls because its P-value is <0.05. Notice that one is interested in keeping those SNPsthat do not reject the null hypothesis. As several SNPs are tested, multiple comparisons must be considered. In this particular setting, a threshold of 0.001 is normally considered. As a quality control measure, it is not necessary to be as conservative as in those situations where false discovery rates need to be controlled.
SNPs that do not pass the HWE test must be removed form further analyses. We can recall setupSNP and indicate the columns of the SNPs to be kept
snps.ok <- rownames(hwe2)[hwe2[,2]>=0.001]
pos <- which(colnames(asthma)%in%snps.ok, useNames = FALSE)
asthma.s <- setupSNP(asthma, pos, sep="")Note that in the variable pos we redefine the SNP variables to be considered as class snp.
5 SNP association analysis
We are interested in finding those SNPs associated with asthma status that is encoded in the variable casecontrol. We first illustrate the association between case-control status and the SNP rs1422993. The association analysis for all genetic models is performed by the function association that regresses casecontrol on the variable rs1422993 from the dataset asthma.s that already contains the SNP variables of class snp.
association(casecontrol ~ rs1422993, data = asthma.s)
SNP: rs1422993 adjusted by:
0 % 1 % OR lower upper p-value AIC
Codominant
G/G 730 59.0 173 50.9 1.00 0.017768 1642
G/T 425 34.3 145 42.6 1.44 1.12 1.85
T/T 83 6.7 22 6.5 1.12 0.68 1.84
Dominant
G/G 730 59.0 173 50.9 1.00 0.007826 1642
G/T-T/T 508 41.0 167 49.1 1.39 1.09 1.77
Recessive
G/G-G/T 1155 93.3 318 93.5 1.00 0.877863 1649
T/T 83 6.7 22 6.5 0.96 0.59 1.57
Overdominant
G/G-T/T 813 65.7 195 57.4 1.00 0.005026 1641
G/T 425 34.3 145 42.6 1.42 1.11 1.82
log-Additive
0,1,2 1238 78.5 340 21.5 1.22 1.01 1.47 0.040151 1644The function association follows the usual syntax of R modelling functions with the difference that the variables in the model that are of class snp are tested using different genetic models. In our example, we observe that all genetic models but the recessive one are statistically significant. association also fits the overdominant model, which compares the two homozygous genotypes versus the heterozygous one. This genetic model of inheritance is biologically rare although it has been linked to sickle cell anemia in humans. The result table describes the number of individuals in each genotype across cases and controls. The ORs and CI-95% are also computed. The last column describes the AIC (Akaike information criteria) that can be used to decide which is the best model of inheritance; the lower the better the model is.
In the example, one may conclude that rs1422993 is associated with asthma and that, for instance, the risk of being asthmatic is 39% higher in people having at least one alternative allele (T) with respect to individuals having none (dominant model). This risk is statistically significant since the CI-95% does not contain 1, the P-value is 0.0078<0.022, or the P-value of the max-statistics is 0.01
maxstat(asthma.s$casecontrol, asthma.s$rs1422993) dominant recessive log-additive MAX-statistic Pr(>z)
[1,] 7.073 0.024 4.291 7.073 0.0182 *
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1If an expected model of inheritance is hypothesized, the association analysis for the model can be specified in the argument model, which by default test all models,
association(casecontrol ~ rs1422993, asthma.s, model="dominant")
SNP: rs1422993 adjusted by:
0 % 1 % OR lower upper p-value AIC
Dominant
G/G 730 59 173 50.9 1.00 0.007826 1642
G/T-T/T 508 41 167 49.1 1.39 1.09 1.77 Association tests are typically adjusted by covariates, which are incorporated in the model in the usual form
association(casecontrol ~ rs1422993 + country + smoke, asthma.s)
SNP: rs1422993 adjusted by: country smoke
0 % 1 % OR lower upper p-value AIC
Codominant
G/G 728 59.1 173 51.0 1.00 0.06940 1408
G/T 423 34.3 144 42.5 1.38 1.05 1.82
T/T 81 6.6 22 6.5 1.06 0.61 1.85
Dominant
G/G 728 59.1 173 51.0 1.00 0.03429 1407
G/T-T/T 504 40.9 166 49.0 1.33 1.02 1.73
Recessive
G/G-G/T 1151 93.4 317 93.5 1.00 0.79338 1411
T/T 81 6.6 22 6.5 0.93 0.54 1.60
Overdominant
G/G-T/T 809 65.7 195 57.5 1.00 0.02147 1406
G/T 423 34.3 144 42.5 1.37 1.05 1.80
log-Additive
0,1,2 1232 78.4 339 21.6 1.19 0.96 1.46 0.11191 1409ORs for stratified analysis on given categorical covariates are used to verify whether the risk is constant across groups
association(casecontrol ~ rs1422993 + survival::strata(gender), asthma.s)
SNP: rs1422993 adjusted by: survival::strata(gender)
0 % 1 % OR lower upper p-value AIC
Codominant
G/G 730 59.0 173 50.9 1.00 0.022940 1634
G/T 425 34.3 145 42.6 1.42 1.11 1.83
T/T 83 6.7 22 6.5 1.09 0.66 1.80
Dominant
G/G 730 59.0 173 50.9 1.00 0.011144 1633
G/T-T/T 508 41.0 167 49.1 1.37 1.07 1.74
Recessive
G/G-G/T 1155 93.3 318 93.5 1.00 0.805330 1640
T/T 83 6.7 22 6.5 0.94 0.58 1.53
Overdominant
G/G-T/T 813 65.7 195 57.4 1.00 0.006378 1632
G/T 425 34.3 145 42.6 1.41 1.10 1.80
log-Additive
0,1,2 1238 78.5 340 21.5 1.21 1.00 1.46 0.055231 1636We can see, for instance, that the dominant model is significant only in males. The subset argument allows fitting the model in a subgroup of individuals
association(casecontrol ~ rs1422993, asthma.s,
subset=country=="Spain")
SNP: rs1422993 adjusted by:
0 % 1 % OR lower upper p-value AIC
Codominant
G/G 179 54.6 22 44.9 1.00 0.3550 295.2
G/T 125 38.1 24 49.0 1.56 0.84 2.91
T/T 24 7.3 3 6.1 1.02 0.28 3.66
Dominant
G/G 179 54.6 22 44.9 1.00 0.2059 293.7
G/T-T/T 149 45.4 27 55.1 1.47 0.81 2.70
Recessive
G/G-G/T 304 92.7 46 93.9 1.00 0.7576 295.2
T/T 24 7.3 3 6.1 0.83 0.24 2.85
Overdominant
G/G-T/T 203 61.9 25 51.0 1.00 0.1502 293.2
G/T 125 38.1 24 49.0 1.56 0.85 2.85
log-Additive
0,1,2 328 87.0 49 13.0 1.23 0.77 1.96 0.3816 294.5These analyses can be also be performed in quantitative traits, such as body mass index, since association function automatically selects the error distribution of the regression analysis (either Gaussian or binomial).
association(bmi ~ rs1422993, asthma.s)
SNP: rs1422993 adjusted by:
n me se dif lower upper p-value AIC
Codominant
G/G 896 25.53 0.1446 0.000000 0.9069 9069
G/T 565 25.50 0.1834 -0.027059 -0.4874 0.4332
T/T 105 25.71 0.4676 0.178076 -0.7057 1.0619
Dominant
G/G 896 25.53 0.1446 0.000000 0.9818 9067
G/T-T/T 670 25.54 0.1710 0.005089 -0.4324 0.4426
Recessive
G/G-G/T 1461 25.52 0.1135 0.000000 0.6694 9067
T/T 105 25.71 0.4676 0.188540 -0.6769 1.0540
Overdominant
G/G-T/T 1001 25.55 0.1383 0.000000 0.8424 9067
G/T 565 25.50 0.1834 -0.045739 -0.4965 0.4050
log-Additive
0,1,2 0.033951 -0.3153 0.3832 0.8489 9067For BMI, association tests whether the difference between means is statistically significant, rather than computing an OR.
For multiple SNP data, our objective is to identify the variants that are significantly associated with the trait. The most basic strategy is, therefore, to fit an association test like the one described above for each of the SNPs in the dataset and determine which of those associations are significant. The massive univariate testing is the most widely used analysis method for omic data because of its simplicity. In SNPassoc, this type of analysis is done with the function WGassociation
ans <- WGassociation(casecontrol, data=asthma.s)
head(ans) comments codominant dominant recessive overdominant log-additive
rs4490198 - 0.52765 0.29503 0.96400 0.29998 0.49506
rs4849332 - 0.96912 0.92986 0.84806 0.82327 0.97049
rs1367179 - 0.62775 0.59205 0.35786 0.86419 0.43994
rs11123242 - 0.68622 0.67596 0.39801 0.92878 0.52009
rs13014858 - 0.52578 0.26739 0.88011 0.34966 0.40897
rs1430094 - 0.13375 0.10569 0.54432 0.04490 0.36611Here, only the outcome is required in the formula argument (first argument) since the function successively calls association on each of the variables of class snp within data. The function returns the P-values of association of each SNP under each genetic model. Covariates can also be introduced in the model
ans.adj <- WGassociation(casecontrol ~ country + smoke, asthma.s)
head(ans.adj)SNPassoc is computationally limited on large genomic data. The computing time can be reduced by parallelization, specifying in the argument mc.cores the number of computing cores to be used. Alternatively, the function scanWGassociation, a C compiled function, can be used to compute a predetermined genetic model across all SNPs, passed in the argument model, which by default is the additive model
ans.fast <- scanWGassociation(casecontrol, asthma.s)NOTE: This function is not available on the SNPassoc version available on CRAN. The user can install the development version available on GitHub to get access to this function just executing
devtools::install_github("isglobal-brge/SNPassoc")The P-values obtained from massive univariate analyses are visualized with the generic plot function
plot(ans)
Figure 4: Manhattan-type plots for different genetic models
P-values in -log10 scale to assess the association between case-control status and SNPs in the asthma example.
This produces a Manhattan plot of the -log10(P-values) for all the SNPs over all models. It shows the nominal level of significance and the Bonferroni level, which is the level corrected by the multiple testing across all SNPs. The overall hypothesis of massive univariate association tests is whether there is any SNP that is significantly associated with the phenotype. As multiple SNPs are tested, the probability of finding at least one significant finding increases if we do not lower the significance threshold. The Bonferroni correction lowers the threshold by the number of SNPs tested (0.0001=0.05/51). In the Manhattan plotof our analysis, we see that no SNP is significant at the Bonferroni level, and therefore there is no SNP that is significantly associated with asthma.
Maximum-statistic (see González et al. (2008)) can also be used to test association between asthma status and SNPs
ans.max <- maxstat(asthma.s, casecontrol)
ans.max dominant recessive log-additive MAX-statistic Pr(>z)
rs4490198 1.097 0.002 0.466 1.097 0.50207
rs4849332 0.008 0.037 0.001 0.037 0.97650
rs1367179 0.287 0.845 0.602 0.845 0.58872
rs11123242 0.175 0.714 0.417 0.714 0.63910
rs13014858 1.230 0.023 0.683 1.230 0.46364
rs1430094 2.617 0.368 0.821 2.617 0.20687
rs1430093 1.051 0.042 0.743 1.051 0.51949
rs746710 0.728 0.679 1.051 1.051 0.51615
rs1430090 0.172 0.463 0.000 0.463 0.74286
rs6737251 0.143 0.156 0.217 0.217 0.86897
rs11685217 0.894 0.030 0.705 0.894 0.56948
rs1430097 0.003 0.183 0.029 0.183 0.88847
rs10496465 0.003 0.020 0.008 0.020 0.98729
rs3756688 0.016 0.738 0.266 0.738 0.62631
rs2303063 0.060 1.271 0.658 1.271 0.45282
rs1422993 7.073 0.024 4.291 7.073 0.01782 *
rs2400478 1.662 0.056 1.055 1.662 0.35902
rs714588 0.659 0.061 0.150 0.659 0.65848
rs1023555 0.221 0.104 0.261 0.261 0.84688
rs898070 0.020 1.794 0.346 1.794 0.33132
rs963218 0.165 0.190 0.263 0.263 0.84374
rs1419835 1.084 0.775 0.295 1.084 0.51082
rs765023 1.959 0.526 0.483 1.959 0.30285
rs1345267 2.582 0.003 1.383 2.582 0.21185
rs324381 0.175 0.402 0.377 0.402 0.77455
rs184448 9.710 2.026 8.253 9.710 0.00309 **
rs324396 2.312 0.188 1.051 2.312 0.24768
rs324957 7.598 2.134 7.157 7.598 0.01322 *
rs324960 2.901 7.928 6.443 7.928 0.01161 *
rs10486657 0.054 0.500 0.001 0.500 0.73041
rs324981 3.168 2.431 4.270 4.270 0.08166 .
rs1419780 0.123 1.193 0.005 1.193 0.47801
rs325462 1.545 1.645 2.412 2.412 0.23233
rs727162 3.022 0.643 3.074 3.074 0.15950
rs10250709 0.737 0.007 0.360 0.737 0.62865
rs6958905 0.490 0.099 0.447 0.490 0.73263
rs10238983 0.094 0.692 0.328 0.692 0.64736
rs4941643 1.294 0.006 0.465 1.294 0.44616
rs3794381 0.127 0.998 0.489 0.998 0.53537
rs2031532 0.025 0.240 0.127 0.240 0.85726
rs2247119 0.379 0.000 0.229 0.379 0.78437
rs8000149 0.020 0.043 0.043 0.043 0.97292
rs2274276 0.005 0.034 0.023 0.034 0.97787
rs7332573 1.247 1.703 1.825 1.825 0.32896
rs3829366 1.137 0.448 0.069 1.137 0.49192
rs6084432 2.999 0.848 3.279 3.279 0.14166
rs512625 2.180 0.030 1.119 2.180 0.26371
rs3918395 0.903 0.414 0.455 0.903 0.57133
rs2787095 0.178 0.069 0.184 0.184 0.88683
rs2853215 0.686 0.931 1.130 1.130 0.49337
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1We note that even under the max-statistics none of the SNPs tested is significant under the Bonferroni correction (<0.0001) for multiple SNP testing
#minimum P-value across SNPs
min(ans.max["Pr(>z)",])[1] 0.003085532Information for specific association models for given SNPs can also be retrieved with WGstats
infoTable <- WGstats(ans)Therefore, we can have access to the results for a given SNP by
infoTable$rs1422993
SNP: rs1422993 adjusted by:
0 % 1 % OR lower upper p-value AIC
Codominant
G/G 730 59.0 173 50.9 1.00 0.017768 1642
G/T 425 34.3 145 42.6 1.44 1.12 1.85
T/T 83 6.7 22 6.5 1.12 0.68 1.84
Dominant
G/G 730 59.0 173 50.9 1.00 0.007826 1642
G/T-T/T 508 41.0 167 49.1 1.39 1.09 1.77
Recessive
G/G-G/T 1155 93.3 318 93.5 1.00 0.877863 1649
T/T 83 6.7 22 6.5 0.96 0.59 1.57
Overdominant
G/G-T/T 813 65.7 195 57.4 1.00 0.005026 1641
G/T 425 34.3 145 42.6 1.42 1.11 1.82
log-Additive
0,1,2 1238 78.5 340 21.5 1.22 1.01 1.47 0.040151 1644recovering our previous results given by association function.
NOTE: The R output of specific association analyses can be exported into LaTeX by using getNiceTable function and xtable R package. The following code creates a table for the SNPs rs1422993 and rs184448
library(xtable)
out <- getNiceTable(ans[c("rs1422993", "rs184448")])
nlines <- attr(out, "nlines")
hlines <- c(-1, -1, 0, cumsum(nlines+1), nrow(out), nrow(out))
print(xtable(out, caption='Genetic association using
different genetic models from asthma
data example of rs1422993 and rs184448
SNPs obtained with SNPassoc.',
label = 'tab-2SNPs'),
tabular.enviroment="longtable", file="tableSNPs",
floating=FALSE, include.rownames = FALSE,
hline.after= hlines, sanitize.text.function=identity)6 Gene-environment and gene-gene interactions
Gene-enviroment (GxE) analyses can be performed within SNPassoc using association function. Assume that we are interested in testing whether the risk of rs1422993 for asthma under the dominant model is different among smokers (variable smoke; 0=never, 1=ever). This code fits a model with an interaction term where the environmental variable is required to be a factor factor variable.
association(casecontrol ~ dominant(rs1422993)*factor(smoke),
data=asthma.s)
SNP: dominant(rs1422993 adjusted by:
Interaction
---------------------
0 OR lower upper 1 OR lower upper
G/G 486 130 1.00 NA NA 242 43 0.66 0.46 0.97
G/T-T/T 354 128 1.35 1.02 1.79 150 38 0.95 0.63 1.42
p interaction: 0.8513
factor(smoke) within dominant(rs1422993
---------------------
G/G
0 1 OR lower upper
0 486 130 1.00 NA NA
1 242 43 0.66 0.46 0.97
G/T-T/T
0 1 OR lower upper
0 354 128 1.0 NA NA
1 150 38 0.7 0.47 1.06
p trend: 0.8513
dominant(rs1422993 within factor(smoke)
---------------------
0
0 1 OR lower upper
G/G 486 130 1.00 NA NA
G/T-T/T 354 128 1.35 1.02 1.79
1
0 1 OR lower upper
G/G 242 43 1.00 NA NA
G/T-T/T 150 38 1.43 0.88 2.31
p trend: 0.8513 The result is an interaction table showing that the risk of individuals carrying the T allele increases the risk of asthma in never smokers (OR=1.35; CI: 1.02-1.79) while it is not significant in ever smokers (OR=0.95; CI: 0.63-1.42). However, the interaction is not statistically significant (\(P\)-interaction=0.8513). The output also shows the stratified ORs that can help in interpreting the results.
In a similar way, gene-gene interaction (GxG) of a given SNP epistasis model can also be fitted using the same function. In that case, the genetic model of the interacting SNP must be indicated in the model.inteaction argument.
association(casecontrol ~ rs1422993*factor(rs184448),
data=asthma.s, model.interaction = "dominant" )
SNP: rs1422993 adjusted by:
Interaction
---------------------
T/T OR lower upper T/G OR lower upper 0 1 G/G lower upper
G/G 227 43 1.00 NA NA 359 96 1.41 0.95 2.10 128 30 1.24 0.74 2.07
G/T-T/T 154 33 1.13 0.69 1.86 265 93 1.85 1.24 2.77 78 38 2.57 1.55 4.27
p interaction: 0.24499
factor(rs184448) within rs1422993
---------------------
G/G
0 1 OR lower upper
T/T 227 43 1.00 NA NA
T/G 359 96 1.41 0.95 2.10
G/G 128 30 1.24 0.74 2.07
G/T-T/T
0 1 OR lower upper
T/T 154 33 1.00 NA NA
T/G 265 93 1.64 1.05 2.55
G/G 78 38 2.27 1.32 3.90
p trend: 0.24499
rs1422993 within factor(rs184448)
---------------------
T/T
0 1 OR lower upper
G/G 227 43 1.00 NA NA
G/T-T/T 154 33 1.13 0.69 1.86
T/G
0 1 OR lower upper
G/G 359 96 1.00 NA NA
G/T-T/T 265 93 1.31 0.95 1.82
G/G
0 1 OR lower upper
G/G 128 30 1.00 NA NA
G/T-T/T 78 38 2.08 1.19 3.62
p trend: 0.12743 We observe that the interaction between these two SNPs is not statistically significant (P-value=0.24). However, the OR of GG genotype of rs184448 differs across individuals between the GG and GT-TT genotypes of rs1422993 (see ORs for GG in the second table of the output).
The user also can perform GxG for a set of SNPs using this code. Let us assume we are interested in assessing interaction between the SNPs that are significant at 10% level
ans <- WGassociation(casecontrol, data=asthma.s)
mask <- apply(ans, 1, function(x) min(x, na.rm=TRUE)<0.1)
sig.snps <- names(mask[mask])
sig.snps [1] "rs1430094" "rs1422993" "rs765023" "rs184448" "rs324396" "rs324957"
[7] "rs324960" "rs324981" "rs727162" "rs6084432"idx <- which(colnames(asthma)%in%sig.snps)
asthma.s2 <- setupSNP(asthma, colSNPs = idx, sep="")
ans.int <- interactionPval(casecontrol ~ 1, data=asthma.s2)
ans.int rs1430094 rs1422993 rs765023 rs184448 rs324396
rs1430094 0.132526514 0.653457029 0.816154586 0.787386835 0.694311497
rs1422993 0.140433948 0.016719949 0.133131712 0.375246182 0.683959376
rs765023 0.171993821 0.144029395 0.182805988 0.961405419 0.194520134
rs184448 0.100074594 0.019963426 0.034666219 0.007969948 0.036825613
rs324396 0.204742661 0.190583402 0.131945703 0.344952544 0.209589962
rs324957 0.103680541 0.019820456 0.034446832 0.696623215 0.318903026
rs324960 0.107216765 0.024180405 0.174801032 0.291457716 0.584132142
rs324981 0.128489057 0.144077239 0.153521356 0.646139555 0.301782199
rs727162 0.258828613 0.240900610 0.188971595 0.173341993 0.120240909
rs6084432 0.214413938 0.187372912 0.187830183 0.264160389 0.252965105
rs324957 rs324960 rs324981 rs727162 rs6084432
rs1430094 0.644661690 0.096913557 0.774083175 0.043758067 0.946641185
rs1422993 0.257661509 0.175946789 0.095251421 0.577504655 0.027437424
rs765023 0.437535350 0.614095008 0.117705086 0.217580773 0.896707843
rs184448 0.018290318 0.356124918 0.311031078 0.297592380 0.349332875
rs324396 0.232076552 0.747574191 0.064231657 0.361336095 0.388626207
rs324957 0.019578585 0.595796247 0.965290164 0.402781904 0.272919867
rs324960 0.404830873 0.017401694 0.168077057 0.406220478 0.725774374
rs324981 0.657378128 0.533095852 0.117043376 0.463436271 0.862291944
rs727162 0.174960014 0.500811687 0.167364803 0.206131411 0.885294485
rs6084432 0.174006927 0.146808311 0.210647392 0.203957720 0.193711884we can visualize the results by
plot(ans.int)