The RNAseqCovarImpute package makes linear model analysis for RNA-seq
read counts compatible with multiple imputation (MI) of missing
covariates. Relying on the Bioconductor limma package,
RNAseqCovarImpute is included in Bioconductor as an extension of the variance modeling at the
observational level (voom) method which can be applied in
circumstances with missing covariate data.
Missing data is a common problem in observational studies, as modeling techniques such as linear regression cannot be fit to data with missing points. Missing data is frequently handled using complete case analyses in which any individuals with missing data are dropped from the study. Dropping participants can reduce statistical power and, in some cases, result in biased model estimates. A common technique to address these problems is to replace or ‘impute’ missing data points with substituted values. Typically, for a given covariate, missing data points are imputed using a prediction model including other relevant covariates as independent variables. In single imputation, a missing value is replaced with the most likely value based on the predictive model. However, by ignoring the uncertainty inherent with predicting missing data, single imputation methods can result in biased coefficients and over-confident standard errors. MI addresses this problem by generating several predictions, thereby allowing for uncertainty about the missing data. In a typical MI procedure: 1) M imputed data sets are created, 2) each data set is analyzed separately (e.g., using linear regression), and 3) estimates and standard errors across the M analyses are pooled using Rubin’s rules. A major problem with implementing MI in RNA sequencing studies is that the outcome data must be included in the imputation prediction models to avoid bias. This is difficult in omics studies with high-dimensional data.
The first method we developed in the RNAseqCovarImpute package
surmounts the problem of high-dimensional outcome data by binning genes
into smaller groups to analyze pseudo-independently. This method
implements covariate MI in gene expression studies by 1) randomly
binning genes into smaller groups, 2) creating M imputed datasets
separately within each bin, where the imputation predictor matrix
includes all covariates and the log counts per million (CPM) for the
genes within each bin, 3) estimating gene expression changes using
limma::voom followed by limma::lmFit
functions, separately on each M imputed dataset within each gene bin, 4)
un-binning the gene sets and stacking the M sets of model results before
applying the limma::squeezeVar function to apply a variance
shrinking Bayesian procedure to each M set of model results, 5) pooling
the results with Rubins’ rules to produce combined coefficients,
standard errors, and P-values, and 6) adjusting P-values for
multiplicity to account for false discovery rate (FDR).
A faster method uses principal component analysis (PCA) to avoid
binning genes while still retaining outcome information in the MI
models. Binning genes into smaller groups requires that the MI and
limma-voom analysis is run many times (typically hundreds). The more
computationally efficient MI PCA method implements covariate MI in gene
expression studies by 1) performing PCA on the log CPM values for all
genes using the Bioconductor PCAtools package, 2) creating
M imputed datasets where the imputation predictor matrix includes all
covariates and the optimum number of PCs to retain (e.g., based on
Horn’s parallel analysis or the number of PCs that account for >80%
explained variation), 3) conducting the standard limma-voom pipeline
with the voom followed by lmFit followed by
eBayes functions on each M imputed dataset, 4) pooling the
results with Rubins’ rules to produce combined coefficients, standard
errors, and P-values, and 5) adjusting P-values for multiplicity to
account for false discovery rate (FDR).
Normally you would have your own covariate and RNA-sequencing data.
We generated random data for the purpose of this demonstration. The
exact code used to generate these data are found in the Example Data for
RNAseqCovarImpute vignette. In short, example_data
contains 500 rows with data for variables x, y, and z, which are
continuous normally distributed, and a and b, which are binary
variables. Missigness was simulated for all variables other than x such
that a complete case analysis would drop 24.2% of participants.
example_DGE contains random count data from the Poisson
distribution for 500 made up genes, ENS1-ENS500
## Loading required package: ggplot2## Loading required package: ggrepel##
## Attaching package: 'PCAtools'## The following objects are masked from 'package:stats':
##
## biplot, screeplotWe demonstrate the MI PCA method first, as it is far faster and performs just as well, or even better in many cases, compared with the original gene binning method.
# We use voom to convert counts to logCPM values, adding 0.5 to all the counts to avoid taking the logarithm of zero, and normalized for library size.
start.pca = Sys.time() # To calculate runtime
pca_data = limma::voom(example_DGE)$E
# Conduct pca
p = PCAtools::pca(pca_data)
# Determine the number of PCs that account for >80% explained variation
which(cumsum(p$variance) > 80)[1]## PC78
## 78# Conduct mice. In practice, m should be much larger (e.g., 10-100)
imp = mice::mice(example_data, m=3)##
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## 5 3 y z a bNow we use our limmavoom_imputed_data_pca function to
run the standard limma-voom pipeline on each MI dataset and then pool
the results with Rubins’ rules. This procedure is run in parallel using
the BiocParallel package with the default back-end. Users can change the
back-end using the BPPARAM argument. This argument is
passed to BiocParallel::bplapply. For instance, below we
specify to run limmavoom_imputed_data_pca in serial. Users
specify the formula for the RNA-seq design matrix for which log
fold-changes will be estimated. For each contrast specified in the
voom_formula, p-values, coefficients, and standard errors are stored
under the “_p”, “_coef” and “_se” columns, respectively.
mi_pca_res = RNAseqCovarImpute::limmavoom_imputed_data_pca(imp = imp,
DGE = example_DGE,
voom_formula = "~x + y + z + a + b",
BPPARAM = SerialParam())
# Display the results for the first 5 genes for the x variable in the model.
mi_pca_res[1:5, grep("^x", colnames(mi_pca_res))]## x_p x_coef x_se
## 1 0.06660109 0.0169437695 0.009223663
## 2 0.94247200 -0.0002608712 0.003613852
## 3 0.15306863 -0.0044461922 0.003108986
## 4 0.34271970 -0.0044535003 0.004691093
## 5 0.74174061 -0.0023224159 0.007044885For a given contrast based on the variables in the design matrix (voom_formula), we arrange the genes from lowest to highest p-value and adjust for FDR.
mi_pca_res_x = mi_pca_res %>%
arrange(x_p) %>%
mutate(x_p_adj = p.adjust(x_p, method = "fdr")) %>%
dplyr::select(probe, x_coef, x_p, x_p_adj)
end.pca = Sys.time() # To calculate runtime
time.pca = end.pca - start.pca # To calculate runtime
# Display the results for the first 5 genes
mi_pca_res_x[1:5,]## probe x_coef x_p x_p_adj
## 1 ENS432 -0.02119264 0.0001718585 0.08592926
## 2 ENS65 -0.02265597 0.0019087375 0.47718437
## 3 ENS239 0.01440360 0.0077394573 0.97996572
## 4 ENS327 -0.01010518 0.0084046181 0.97996572
## 5 ENS411 0.02130216 0.0117263716 0.97996572The default is approximately 1 gene per 10 individuals in the study, but the user can specify a different ratio. For example, in a study with 500 participants and 10,000 genes, 200 bins of 50 genes would be created using the default ratio. This example demonstrates why this method can be computationally intensive: the MI and limma-voom analysis will be conducted separately 200 times. When the total number of genes is not divisible by the bin size, the method flexibly creates bins of different sizes. The order of the features (e.g., ENSEMBL gene identifiers) should be randomized before binning.
# Get back the original example_data without the PCs appended
data(example_data)
start.old.method = Sys.time() # To calculate runtime
intervals <- get_gene_bin_intervals(example_DGE, example_data, n = 10)| start | end | number |
|---|---|---|
| 1 | 50 | 50 |
| 51 | 100 | 50 |
| 101 | 150 | 50 |
| 151 | 200 | 50 |
| 201 | 250 | 50 |
| 251 | 300 | 50 |
| 301 | 350 | 50 |
| 351 | 400 | 50 |
| 401 | 450 | 50 |
| 451 | 500 | 50 |
Our goal is to bin genes randomly, so we must randomize the order of the genes in our DGE list. Without this step, genes would be binned together based on their sequential order within the chosen gene annotation (e.g., ENSEMBL or ENTREZ).
Data are imputed using the mice R package with its default predictive modeling methods, which are predictive mean matching, logistic regression, polytomous regression, and proportional odds modeling for continuous, binary, categorical, and unordered variables, respectively. The user may specify “m”, the number of imputed datasets, and “maxit”, the number of iterations for each imputation (default = 10). M imputed datasets are created separately for each gene bin, where the imputation predictor matrix includes all covariates along with the log-CPM for all the genes in a particular bin. Thus, each gene bin contains M sets of imputed data.
The impute_by_gene_bin function loops through a DGE list
using the gene bin intervals from the
get_gene_bin_intervals function. It returns a list of sets
of m imputed datasets, one per gene bin. For instance, if m = 100 and
intervals contains 200 gene bin intervals, output will be a list of 200
sets of 100 imputed datasets. Each of the 200 sets are imputed using
only the genes in one gene bin.
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## 10 3 y z a bThis procedure is run in parallel using the BiocParallel package with
the default back-end. Users can change the back-end using the
BPPARAM argument. This argument is passed to
BiocParallel::bplapply. For instance, to run
gene_bin_impute in serial:
gene_bin_impute <- impute_by_gene_bin(example_data,
intervals,
example_DGE,
m = 3,
BPPARAM = SerialParam()
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## 9 3 y z a b
## 10 1 y z a b
## 10 2 y z a b
## 10 3 y z a b
##
## iter imp variable
## 1 1 y z a b
## 1 2 y z a b
## 1 3 y z a b
## 2 1 y z a b
## 2 2 y z a b
## 2 3 y z a b
## 3 1 y z a b
## 3 2 y z a b
## 3 3 y z a b
## 4 1 y z a b
## 4 2 y z a b
## 4 3 y z a b
## 5 1 y z a b
## 5 2 y z a b
## 5 3 y z a b
## 6 1 y z a b
## 6 2 y z a b
## 6 3 y z a b
## 7 1 y z a b
## 7 2 y z a b
## 7 3 y z a b
## 8 1 y z a b
## 8 2 y z a b
## 8 3 y z a b
## 9 1 y z a b
## 9 2 y z a b
## 9 3 y z a b
## 10 1 y z a b
## 10 2 y z a b
## 10 3 y z a bThe limmavoom_imputed_data_list function loops through
the imputed data list (output from impute_by_gene_bin
function) and runs RNA-seq analysis with the limma-voom pipeline. Users
specify the formula for the RNA-seq design matrix for which log
fold-changes will be estimated. This procedure can also be run with a
different parallel back-end or in serial using the BPPARAM
argument as above.
The final step is to combine the results from each imputed dataset
using Rubin’s rules. The argument “model_results” is the output from the
limmavoom_imputed_data_list function above. The
combine_rubins function applies the squeezeVar
function before pooling results. The result is a table with one row per
gene. The table includes coefficients (e.g., logFC values) standard
errors, degrees of freedom, t-statistics, P-Values, and adjusted
P-values from the limma-voom pipeline. Both the raw and empirical Bayes
moderated statistics are reported. The user selects the predictor of
interest in the form of a linear model contrast for which model results
will be extracted. For a continuous variable this is just the predictor
name. For a categorical variable like b in
example_data we could specify predictor = b1
to get the effect of being in the b = 1 versus the b = 0 group.
final_res <- combine_rubins(
DGE = example_DGE,
model_results = coef_se,
predictor = "x"
)
end.old.method = Sys.time() # To calculate runtime
time.old.method = end.old.method - start.old.method| probe | coef_combined | combined_p_bayes | combined_p_adj_bayes |
|---|---|---|---|
| ENS432 | -0.021 | 0.000 | 0.094 |
| ENS65 | -0.023 | 0.002 | 0.450 |
| ENS327 | -0.011 | 0.005 | 0.827 |
| ENS239 | 0.014 | 0.008 | 0.984 |
| ENS411 | 0.022 | 0.011 | 0.984 |
| ENS260 | 0.011 | 0.015 | 0.984 |
| ENS107 | 0.007 | 0.020 | 0.984 |
| ENS291 | 0.017 | 0.022 | 0.984 |
| ENS219 | 0.012 | 0.024 | 0.984 |
| ENS458 | 0.014 | 0.026 | 0.984 |
The old method took more time(time.old.method) compared
with the MI PCA method (time.pca).
## R version 4.4.2 (2024-10-31)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.1 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=C
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: Etc/UTC
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] PCAtools_2.19.0 ggrepel_0.9.6 ggplot2_3.5.1
## [4] BiocParallel_1.41.0 RNAseqCovarImpute_1.5.0 mice_3.17.0
## [7] edgeR_4.5.0 limma_3.63.2 tidyr_1.3.1
## [10] stringr_1.5.1 dplyr_1.1.4 BiocStyle_2.35.0
##
## loaded via a namespace (and not attached):
## [1] tidyselect_1.2.1 fastmap_1.2.0
## [3] rsvd_1.0.5 digest_0.6.37
## [5] rpart_4.1.23 lifecycle_1.0.4
## [7] survival_3.7-0 statmod_1.5.0
## [9] magrittr_2.0.3 compiler_4.4.2
## [11] rlang_1.1.4 sass_0.4.9
## [13] tools_4.4.2 utf8_1.2.4
## [15] yaml_2.3.10 knitr_1.49
## [17] dqrng_0.4.1 S4Arrays_1.7.1
## [19] DelayedArray_0.33.2 plyr_1.8.9
## [21] abind_1.4-8 withr_3.0.2
## [23] purrr_1.0.2 BiocGenerics_0.53.3
## [25] sys_3.4.3 nnet_7.3-19
## [27] grid_4.4.2 stats4_4.4.2
## [29] fansi_1.0.6 jomo_2.7-6
## [31] beachmat_2.23.2 colorspace_2.1-1
## [33] scales_1.3.0 iterators_1.0.14
## [35] MASS_7.3-61 cli_3.6.3
## [37] crayon_1.5.3 rmarkdown_2.29
## [39] generics_0.1.3 reshape2_1.4.4
## [41] DelayedMatrixStats_1.29.0 minqa_1.2.8
## [43] cachem_1.1.0 zlibbioc_1.52.0
## [45] splines_4.4.2 parallel_4.4.2
## [47] XVector_0.47.0 BiocManager_1.30.25
## [49] matrixStats_1.4.1 vctrs_0.6.5
## [51] boot_1.3-31 glmnet_4.1-8
## [53] Matrix_1.7-1 jsonlite_1.8.9
## [55] BiocSingular_1.23.0 IRanges_2.41.1
## [57] S4Vectors_0.45.2 mitml_0.4-5
## [59] irlba_2.3.5.1 maketools_1.3.1
## [61] locfit_1.5-9.10 foreach_1.5.2
## [63] jquerylib_0.1.4 glue_1.8.0
## [65] nloptr_2.1.1 pan_1.9
## [67] codetools_0.2-20 cowplot_1.1.3
## [69] stringi_1.8.4 shape_1.4.6.1
## [71] gtable_0.3.6 ScaledMatrix_1.15.0
## [73] lme4_1.1-35.5 munsell_0.5.1
## [75] tibble_3.2.1 pillar_1.9.0
## [77] htmltools_0.5.8.1 R6_2.5.1
## [79] sparseMatrixStats_1.19.0 evaluate_1.0.1
## [81] lattice_0.22-6 backports_1.5.0
## [83] broom_1.0.7 bslib_0.8.0
## [85] Rcpp_1.0.13-1 SparseArray_1.7.2
## [87] nlme_3.1-166 xfun_0.49
## [89] MatrixGenerics_1.19.0 buildtools_1.0.0
## [91] pkgconfig_2.0.3