# NEBULA v1.2.0

## Overview

The R package, nebula, provides fast algorithms for fitting negative binomial and Poisson mixed models for analyzing large-scale multi-subject single-cell data. The package nebula accounts for the hierarchical structure of the data by decomposing the total overdispersion into between-subject and within-subject components using a negative binomial mixed model (NBMM). The package nebula can be used for e.g., identifying marker genes, testing treatment effects, detecting genes with differential expression, performing cell-level co-expression analysis, and obtaining Pearson residuals for downstream analyses.

More details can be found in the manuscript “NEBULA: a fast negative binomial mixed model for differential expression and co-expression analyses of large-scale multi-subject single-cell data” (https://www.nature.com/articles/s42003-021-02146-6).

## Installation

install.packages("devtools")
library(devtools)
install_github("lhe17/nebula")

Because the package nebula uses the R package Rfast, the installation process may first install Rfast, which requires that GSL is installed or available in the environment. The installation also requires Rcpp-1.0.7 and has been tested on R-4.1.0. Starting from this version, nebula does not support R-3.6 or an older version of R.

## Functions

The current version provides the following functions.

• nebula: performs an association analysis using NBMMs given a count matrix and subject IDs.
• group_cell: reorders cells to group them by the subject IDs.
• nbresidual: extracts Pearson residuals from the fitted model.

## Basic usage

We use an example data set to illustrate how to use nebula to perform an association analysis of multi-subject single-cell data. The example data set attached to the R package can be loaded as follows.

library(nebula)
data(sample_data)

The example data set includes a count matrix of 6030 cells and 10 genes from 30 subjects.

dim(sample_data$count) #> [1] 10 6176 The count matrix can be a matrix object or a sparse dgCMatrix object. The elements should be integers. sample_data$count[1:5,1:5]
#> 5 x 5 sparse Matrix of class "dgCMatrix"
#>
#> A . . . . .
#> B . . . . .
#> C . 1 2 . .
#> D . . . . .
#> E . . . . .

The subject IDs of each cell are stored in sample_data$sid. The subject IDs can be a character or numeric vector, the length of which should equal the number of cells. head(sample_data$sid)
#> [1] "1" "1" "1" "1" "1" "1"
table(sample_data$sid) #> #> 1 10 11 12 13 14 15 16 17 18 19 2 20 21 22 23 24 25 26 27 #> 187 230 185 197 163 216 211 195 200 239 196 223 198 202 213 210 199 214 237 200 #> 28 29 3 30 4 5 6 7 8 9 #> 205 183 222 191 205 225 211 197 215 207 The next step is to build a design matrix for the predictors. The example data set includes a data frame consisting of three predictors stored in sample_data$pred. To build the design matrix, we can use the function model.matrix. The intercept term must be included in the design matrix.

head(sample_data$pred) #> X1 X2 cc #> 1 0.6155094 0.9759191 control #> 2 1.4608092 0.9759191 case #> 3 1.6675054 0.9759191 control #> 4 -0.1717715 0.9759191 case #> 5 0.2277492 0.9759191 control #> 6 -0.2635516 0.9759191 control df = model.matrix(~X1+X2+cc, data=sample_data$pred)
#>   (Intercept)         X1        X2 cccontrol
#> 1           1  0.6155094 0.9759191         1
#> 2           1  1.4608092 0.9759191         0
#> 3           1  1.6675054 0.9759191         1
#> 4           1 -0.1717715 0.9759191         0
#> 5           1  0.2277492 0.9759191         1
#> 6           1 -0.2635516 0.9759191         1

The association analysis between the gene expression and the predictors can then be conducted using the function nebula. The count matrix is an M by N matrix, where M is the number of genes, and N is the number of cells.

re = nebula(sample_data$count,sample_data$sid,pred=df)
#> Remove  0  genes having low expression.
#> Analyzing  10  genes with  30  subjects and  6176  cells.
re
#> $summary #> logFC_(Intercept) logFC_X1 logFC_X2 logFC_cccontrol se_(Intercept) #> 1 -1.902455 -0.016755225 -0.097867225 0.047278197 0.06335820 #> 2 -2.046638 -0.002679074 -0.053812464 -0.022293899 0.06181112 #> 3 -2.033211 0.017954707 0.002398445 -0.048296661 0.08695028 #> 4 -2.008542 -0.005698984 -0.027780387 0.077357703 0.05509711 #> 5 -1.979437 0.011557090 -0.025198987 0.032890493 0.06155853 #> 6 -1.949991 0.013483039 -0.012548791 -0.031590577 0.07440949 #> 7 -1.969248 -0.003531361 0.075230699 -0.009075031 0.06185028 #> 8 -1.964371 0.013639930 -0.061302756 -0.059284665 0.07786361 #> 9 -2.072699 -0.017372176 -0.043828288 0.026624998 0.05737632 #> 10 -2.045646 0.030742876 0.022260805 -0.025516032 0.06842796 #> se_X1 se_X2 se_cccontrol p_(Intercept) p_X1 p_X2 #> 1 0.03534659 0.06449424 0.06879634 4.362617e-198 0.6354810 0.1291514 #> 2 0.03787429 0.06255849 0.07385888 2.052788e-240 0.9436079 0.3896819 #> 3 0.03696089 0.09238230 0.07258521 6.275230e-121 0.6271261 0.9792875 #> 4 0.03704556 0.05624824 0.07252600 5.822948e-291 0.8777381 0.6213846 #> 5 0.03750948 0.06101307 0.07331551 7.432319e-227 0.7579977 0.6795995 #> 6 0.03623477 0.07321208 0.07087566 2.257914e-151 0.7098168 0.8639067 #> 7 0.03631619 0.06068697 0.07133730 1.872102e-222 0.9225364 0.2151043 #> 8 0.03551903 0.07955877 0.06969748 1.957495e-140 0.7009654 0.4409831 #> 9 0.03816039 0.05767972 0.07453316 9.307495e-286 0.6489358 0.4473406 #> 10 0.03798694 0.06917485 0.07374591 2.292903e-196 0.4183419 0.7476005 #> p_cccontrol gene_id gene #> 1 0.4919443 1 A #> 2 0.7627706 2 B #> 3 0.5058082 3 C #> 4 0.2861434 4 D #> 5 0.6537089 5 E #> 6 0.6558008 6 F #> 7 0.8987718 7 G #> 8 0.3949916 8 H #> 9 0.7209245 9 I #> 10 0.7293432 10 J #> #>$overdispersion
#>       Subject      Cell
#> 1  0.08125256 0.8840821
#> 2  0.07102681 0.9255032
#> 3  0.17159404 0.9266395
#> 4  0.05026165 0.8124118
#> 5  0.07075366 1.2674146
#> 6  0.12086392 1.1096065
#> 7  0.07360445 0.9112956
#> 8  0.13571262 0.7549629
#> 9  0.05541398 0.8139652
#> 10 0.09496649 0.9410035
#>
#> $convergence #> [1] 1 1 1 1 1 1 1 1 1 1 #> #>$algorithm
#>  [1] "NBGMM (LN)" "NBGMM (LN)" "NBGMM (LN)" "NBGMM (LN)" "NBGMM (LN)"
#>  [6] "NBGMM (LN)" "NBGMM (LN)" "NBGMM (LN)" "NBGMM (LN)" "NBGMM (LN)"
#>
#> $covariance #> NULL The function by default fitted the negative binomial gamma mixed model (NBGMM) for each of the genes, and return a list of summary statistics including the fold change, p-values, and both subject-level and cell-level overdispersions ($$\sigma^2$$ and $$\phi^{-1}$$). The cells need to be grouped by the subjects (that is, the cells of the same subject should be placed consecutively) before using as the input to the nebula function. If the cells are not grouped, the group_cell function can be used to first reorder the cells, as shwon below. If a scaling factor is specified by the user, it should also be included in group_cell. If the cells are already grouped, group_cell will return NULL. ### Example data_g = group_cell(count=sample_data$count,id=sample_data$sid,pred=df) re = nebula(data_g$count,data_g$id,pred=data_g$pred)

If pred is not specified, nebula will fit the model with an intecept term by default. This can be used when only the overdispersions are of interest.

## Specifying scaling factors

The scaling factor for each cell is specified in nebula using the argument offset. The argument offset has to be a vector of length N containing positive values. Note that log(offset) will be the offset term in the NBMM. Common scaling factors can be the library size of a cell or a normalizing factor adjusted using e.g., TMM. If not specified, nebula will set offset as one by default, which means that each cell is treated equally. If the input count matrix is already normalized by another tool, e.g., scTransform, then you should not specify offset. However, since nebula directly models the raw counts, it is not recommended to use a normalized count matrix for nebula.

re = nebula(sample_data$count,sample_data$sid,pred=df,offset=sample_data$offset) ## Difference between NEBULA-LN and NEBULA-HL In nebula, a user can choose one of the two algorithms to fit an NBGMM. NEBULA-LN uses an approximated likelihood based on the law of large numbers, and NEBULA-HL uses an h-likelihood. A user can select these methods through method='LN' or method='HL'. NEBULA-LN is faster and performs particularly well when the number of cells per subject (CPS) is large. In addition, NEBULA-LN is much more accurate in estimating a very large subject-level overdispersion. In contrast, NEBULA-HL is slower but more accurate in estimating the cell-level overdispersion. In the following analysis of the example data set comprising ~200 cells per subject, the difference of the estimated cell-level overdispersions between NEBULA-LN and NEBULA-HL is ~5% for most genes. re_ln = nebula(sample_data$count,sample_data$sid,pred=df,offset=sample_data$offset,method='LN')
#> Remove  0  genes having low expression.
#> Analyzing  10  genes with  30  subjects and  6176  cells.
re_hl = nebula(sample_data$count,sample_data$sid,pred=df,offset=sample_data$offset,method='HL') #> Remove 0 genes having low expression. #> Analyzing 10 genes with 30 subjects and 6176 cells. ## compare the estimated overdispersions cbind(re_hl$overdispersion,re_ln$overdispersion) #> Subject Cell Subject Cell #> 1 0.08432326 0.9284701 0.08125256 0.8840821 #> 2 0.07455465 0.9726512 0.07102681 0.9255032 #> 3 0.17403264 0.9817571 0.17159404 0.9266395 #> 4 0.05352150 0.8516682 0.05026165 0.8124118 #> 5 0.07480034 1.3254379 0.07075366 1.2674146 #> 6 0.12372426 1.1653128 0.12086392 1.1096065 #> 7 0.07724823 0.9578170 0.07360445 0.9112956 #> 8 0.13797636 0.7991950 0.13571262 0.7549629 #> 9 0.05879485 0.8568851 0.05541398 0.8139652 #> 10 0.09782324 0.9940222 0.09496649 0.9410035 Such difference has little impact on testing fixed-effects predictors under this sample size. ## compare the p-values for testing the predictors using NEBULA-LN and NEBULA-HL cbind(re_hl$summary[,10:12],re_ln$summary[,10:12]) #> p_X1 p_X2 p_cccontrol p_X1 p_X2 p_cccontrol #> 1 0.6373037 0.1346299 0.4950795 0.6354810 0.1291514 0.4919443 #> 2 0.9444825 0.3977109 0.7626827 0.9436079 0.3896819 0.7627706 #> 3 0.6282384 0.9787881 0.5087304 0.6271261 0.9792875 0.5058082 #> 4 0.8786074 0.6278827 0.2868256 0.8777381 0.6213846 0.2861434 #> 5 0.7596198 0.6872259 0.6544751 0.7579977 0.6795995 0.6537089 #> 6 0.7134192 0.8656686 0.6576835 0.7098168 0.8639067 0.6558008 #> 7 0.9216994 0.2230963 0.8977251 0.9225364 0.2151043 0.8987718 #> 8 0.7017083 0.4443602 0.3955343 0.7009654 0.4409831 0.3949916 #> 9 0.6505414 0.4561467 0.7238322 0.6489358 0.4473406 0.7209245 #> 10 0.4199828 0.7510836 0.7308108 0.4183419 0.7476005 0.7293432 The bias of NEBULA-LN in estimating the cell-level overdispersion gets larger when the CPS value becomes lower or the gene expression is more sparse. If the CPS value is <30, nebula will set method='HL' regardless of the user’s input. When NEBULA-LN is used, the user can opt for better accuracy of estimating a smaller subject-level overdispersion through the argument $$\kappa$$. NEBULA first fits the data using NEBULA-LN. If the estimated $$\kappa$$ for a gene is smaller than the user-defined value, NEBULA-HL will be used to estimate the subject-level overdispersion for the gene. The default value of $$\kappa$$ is 800, which can provide a good estimate of the subject-level overdispersion as low as ~0.005. Our simulation results suggest that $$\kappa=200$$ is often sufficent for achieving a well controlled false positive rate of testing a cell-level predictor. We do not recommend using a smaller $$\kappa$$ than 200. Specifying a larger $$\kappa$$ can obtain a more accurate estimate of a smaller subject-level overdispersion when the cell-level overdispersion is large, but will be computationally slower. On the other hand, testing a subject-level predictor (i.e., a variable whose values are shared across all cells from a subject, such as age, sex, treatment, genotype, etc) is more sensitive to the accuracy of the estimated subject-level overdispersion. So we recommend using $$\kappa=800$$ (as default) or even larger when testing a subject-level predictor. Another option to testing a subject-level predictor is to use a Poisson gamma mixed model, which is extremely fast (>50x faster than NEBULA-LN) and will be described below. ## Filtering low-expression genes NEBULA-HL automatically uses a higher-order Laplace approximation for low-expressed genes of which the average count per subject is less than 3. The higher-order Laplace approximation substantailly increases the accuracy for estimating the subject-level overdispersion for low-expressed genes and controls the false positive rate. Nevertheless, we recommend removing genes with very low expression from the analysis because there is little statistical power for these genes. Filtering out low-expressed genes can be specified by cpc=0.005 (i.e., counts per cell<0.5%). The argument cpc is defined by the ratio between the total count of the gene and the number of cells. ## Checking convergence for the summary statistics and quality control nebula reports convergence information about the estimation algorithm for each gene along with the summary statistics. This is useful and important information for quality control to filter out genes of which the estimation procedure potentially does not converge. Generally, a convergence code $$\leq$$ -20 suggests that the algorithm does not converge well. If the convergence code is -30, which indicates a failure of convergence, their summary statistics should NOT be used. If the convergence code is -20 or -40, it indicates that the optimization algorithm stops at the maximum step limit before the complete convergence. The results should be interpreted with caution in this case. The failure of convergence may occur when the sample size is very small, there are too few positive counts, or the gene has huge overdispersions, in which case the likelihood is flat or the optimization is sensitive to the initial values. For those genes that have a bad convergence code, in many cases, trying a different negative binomial mixed model (e.g., NBLMM, see below for more details) may solve the problem. Depending on the concrete application, the estimated gene-specific overdispersions can also be taken into consideration in quality control. For example, when testing differential expression for a variable, genes with a very large estimated cell-level overdispersion should be filtered out because such genes have huge unexplained noises. A large cell-level overdispersion is generally rare in UMI-based single cell data, especially among abundantly expressed genes, but more common in e.g., SMART-seq2 as PCR duplicates introduce substantial noises. It might be hard to give a precise cut-off for a large overdispersion because it also depends on the sample size of the data. Based on the empirical simulation study in (https://www.nature.com/articles/s42003-021-02146-6), genes with an estimated cell-level overdispersion >100 should be removed for a data set with at least 50 cells per subject. On the other hand, if the purpose is to extract residuals for downstream analysis such as clustering, genes with a large cell-level overdispersion might be preferable because they have large variations. If the variable of interest is subject-level, genes with a very large subject-level overdispersion (>1) should be removed or interpreted cautiously as well. In addition, at least a moderate number of subjects (>30) are required for testing a subject-level variable using nebula simply because a small number of subjects are not enough to accurately estimate the subject-level overdispersion. As shown in the original article, even 30 subjects lead to mild inflated type I errors in most simulated scenarios. If the number of subjects is small, methods accounting for small sample size (e.g., DESeq2, edgeR) should be used for testing subject-level variables. ## Using other mixed models In addition to the NBGMM, the nebula package provides efficient estimation implementation for a Poisson gamma mixed model and a negative binomial lognormal mixed model (NBLMM). This can be specified through model="PMM" and model="NBLMM", respectively. The NBLMM is the same model as that adopted in the glmer.nb function in the lme4 R package, but is computationally much more efficient by setting method='LN'. The only difference between NBGMM and NBLMM is that NBGMM uses a gamma distribution for the random effects while the NBLMM uses a lognormal distribution. The PMM is the fastest among these models. Note that the Poisson mixed model (PMM) should not be used to test a cell-level predictor because it only estimates the subject-level overdispersion. Here is an example of using the PMM to fit the example data set. ### Example re = nebula(sample_data$count,sample_data$sid,pred=df,offset=sample_data$offset,model='PMM')
#> Remove  0  genes having low expression.
#> Analyzing  10  genes with  30  subjects and  6176  cells.
logFC_(Intercept) logFC_X1 logFC_X2 logFC_cccontrol se_(Intercept) se_X1 se_X2 se_cccontrol p_(Intercept) p_X1 p_X2 p_cccontrol gene_id gene
-1.903571 -0.0155809 -0.0976660 0.0511060 0.0661297 0.0329115 0.0655553 0.0642299 0 0.6359142 0.1362700 0.4262222 1 A
-2.047864 -0.0032670 -0.0536887 -0.0189269 0.0644332 0.0355074 0.0635450 0.0694853 0 0.9266904 0.3981703 0.7853239 2 B
-2.032645 0.0179777 0.0009387 -0.0505390 0.0908196 0.0345496 0.0932449 0.0676706 0 0.6028248 0.9919678 0.4551611 3 C
-2.009746 -0.0054963 -0.0278602 0.0782074 0.0573209 0.0350745 0.0574459 0.0686939 0 0.8754792 0.6276889 0.2549156 4 D
-1.980528 0.0106338 -0.0248791 0.0312190 0.0644287 0.0343355 0.0621576 0.0671645 0 0.7567865 0.6889656 0.6420644 5 E
-1.950451 0.0160341 -0.0134775 -0.0345244 0.0778198 0.0333858 0.0738508 0.0650410 0 0.6310363 0.8551928 0.5955505 6 F
-1.970271 -0.0026753 0.0750060 -0.0063677 0.0645989 0.0341936 0.0615160 0.0668723 0 0.9376369 0.2227329 0.9241391 7 G
-1.964311 0.0141532 -0.0610984 -0.0578672 0.0809943 0.0336579 0.0800990 0.0656800 0 0.6741202 0.4455910 0.3782927 8 H
-2.074031 -0.0178190 -0.0436094 0.0259745 0.0597947 0.0362203 0.0587679 0.0707912 0 0.6227459 0.4580494 0.7136813 9 I
-2.046055 0.0307026 0.0227238 -0.0246112 0.0714158 0.0354844 0.0702268 0.0691813 0 0.3869068 0.7462578 0.7220276 10 J

## Testing contrasts

In some situations, a user may want to test a combination (contrast) of the log(FC) or perform a global test for multiple variables or levels. For example, a user may want to test whether the log(FC) of two variables are the same. Here, we show how nebula can be used for this kind of analysis.

The first step is to tell nebula to output the covariance matrix of the estimated log(FC). This can be done by specifying covariance=TRUE in nebula. To save storage, the covariance returned by nebula only contains the elements in the lower triangular part including the diagonal. Here is an example to recover the covariance matrix from the output of nebula.

df = model.matrix(~X1+X2+cc, data=sample_data$pred) re_ln = nebula(sample_data$count,sample_data$sid,pred=df,offset=sample_data$offset,method='LN',covariance=TRUE)
#> Remove  0  genes having low expression.
#> Analyzing  10  genes with  30  subjects and  6176  cells.
cov= matrix(NA,4,4)
cov[lower.tri(cov,diag=T)] = as.numeric(re_ln$covariance[1,]) cov[upper.tri(cov)] = t(cov)[upper.tri(cov)] cov #> [,1] [,2] [,3] [,4] #> [1,] 4.014261e-03 2.499051e-05 1.384999e-04 -5.197643e-05 #> [2,] 2.499051e-05 1.249382e-03 9.212341e-06 -1.167080e-05 #> [3,] 1.384999e-04 9.212341e-06 4.159507e-03 5.142249e-05 #> [4,] -5.197643e-05 -1.167080e-05 5.142249e-05 4.732936e-03 Note that if there are K variables, the covariance table in the output will have (K+1)K/2 columns. So, for a large K, substantial increase of computational intensity should be expected. The second step is to build the contrast vector for your hypothesis. In this example, we want to test whether the log(FC) of X1 and X2 are equal for the first gene. This hypothesis leads to the contrast vector (0 1 -1 0). Thus, the test can be performed using the following code. df = model.matrix(~X1+X2+cc, data=sample_data$pred)
## the gene to test
gene_i = 1
## output covariance
re_ln = nebula(sample_data$count,sample_data$sid,pred=df,offset=sample_data$offset,method='LN',covariance=TRUE) #> Remove 0 genes having low expression. #> Analyzing 10 genes with 30 subjects and 6176 cells. ## recover the covariance matrix cov= matrix(NA,4,4) cov[lower.tri(cov,diag=T)] = as.numeric(re_ln$covariance[gene_i,])
cov[upper.tri(cov)] = t(cov)[upper.tri(cov)]
## build the contrast vector
contrast = c(0,1,-1,0)
## testing the hypothesis
eff = sum(contrast*re_ln$summary[gene_i,1:4]) p = pchisq(eff^2/(t(contrast)%*%cov%*%contrast),1,lower.tail=FALSE) p #> [,1] #> [1,] 0.2692591 ## Extracting Pearson residuals from the negative binomial mixed model Pearson residuals are the distances between the raw count and its expected value standardized by its standard deviation. Pearson residuals obtained from fitting the NBMM can be used for normalization and downstream analyses. The current version (v1.2.0) outputs the marginal Pearson residuals, which regress out only the fixed-effect variables. The next version will be providing the conditional Pearson residuals, which further adjust for the subject-level random effects. The conditional Pearson residuals are very useful in a situation where one needs to remove the subject-level batch effects from the normalized residuals for downstream analyses. The Pearson residuals can be easily extracted by using the nbresidual function after successfully running the nebula function. In nbresidual, you should provide the object returned by the nebula function together with the same arguments including the count matrix, id, pred and offset used in running the nebula function. re = nebula(sample_data$count,sample_data$sid,pred=df,offset=sample_data$offset)
pres = nbresidual(re,count=sample_data$count,id=sample_data$sid,pred=df,offset=sample_data$offset) The parameters count, id, pred and offset should be the same in these two functions. Then, the marginal Pearson residuals are in the matrix pres$residuals. The rows in pres\$residuals correspond to the genes in the output of nebula, and the columns are the cells in count.