IFAA

IFAA is a robust approach to make inference on the association of covariates with the absolute abundance (AA) of microbiome in an ecosystem. It can be also directly applied to relative abundance (RA) data to make inference on AA because the ratio of two RA is equal ratio of their AA. This algorithm can estimate and test the associations of interest while adjusting for potential confounders. High-dimensional covariates are handled with regularization. The estimates of this method have easy interpretation like a typical regression analysis. High-dimensional covariates are handled with regularization and it is implemented by parallel computing. False discovery rate is automatically controlled by this approach. Zeros do not need to be imputed by a positive value for the analysis. The IFAA package also offers the ‘MZILN’ function for estimating and testing associations of abundance ratios with covariates.

The following mixed effect model is used for the association: \[ \log(\mathcal{Y}_i^k)|\mathcal{Y}_i^k>0=\beta^{0k}+X_i^T\beta^k+W_i^T\gamma^k+Z_i^Tb_i+\epsilon_i^k,\hspace{0.2cm}k=1,...,K+1, \] where

The challenge in microbiome analysis is that we can not oberve \(\mathcal{Y}_i^k\). What is observed is its small proportion: \(Y_i^k=C_i\mathcal{Y}^k_i\) where \(C_i\) is an unknown number between 0 and 1 that denote the observed proportion. The IFAA method successfuly addressed this challenge.

Package installation

To install, type the following command in R console:

install.packages("IFAA", repos = "http://cran.us.r-project.org")

The package could be also installed from GitHub using the following code:

require(devtools)
devtools::install_github("gitlzg/IFAA")

Input for IFAA() function

Most of the time, users just need to feed the first five inputs to the function: MicrobData, CovData, linkIDname, testCov and ctrlCov. All other inputs can just take their default values. Below are all the inputs of the functions

MicrobData: Microbiome data matrix containing microbiome absolute abundance or relative abundance with each row per sample and each column per taxon/OTU/ASV (or any other unit). The data matrix can have zero-valued data points. It should also contain an id variable to be linked with the id variable in the covariates data: CovData. This argument can also take file directory path. For example, MicrobData="C://...//microbiomeData.tsv".
CovData: Covariates data matrix containing covariates and confounders with each row per sample and each column per variable. Any categorical variable should be converted into dummy variables in this data matrix unless it can be treated as a continuous variable. It should also contain an id variable to be linked with the id variable in the microbiome data: MicrobData. This argument can also take file directory path. For example, CovData="C://...//covariatesData.tsv".
linkIDname: The common variable name of the id variable in both MicrobData and CovData. The two data sets will be merged by this id variable.
testCov: Covariates that are of primary interest for testing and estimating the associations. It corresponds to \(X_i\) in the equation. Default is NULL which means all covariates are testCov.
ctrlCov: Potential confounders that will be adjusted in the model. It corresponds to \(W_i\) in the equation. Default is NULL which means all covariates except those in testCov are adjusted as confounders.
testMany: This takes logical value TRUE or FALSE. If TRUE, the testCov will contain all the variables in CovData provided testCov is set to be NULL. The default value is TRUE which does not do anything if testCov is not NULL.
ctrlMany: This takes logical value TRUE or FALSE. If TRUE, all variables except testCov are considered as control covariates provided ctrlCov is set to be NULL. The default value is FALSE.
nRef: The number of randomly picked reference taxa used in phase 1. Default number is 40.
nRefMaxForEsti: The maximum number of final reference taxa used in phase 2. The default is 2.
refTaxa: A vector of taxa names. These are reference taxa specified by the user to be used in phase 1 if the user believe these taxa are indepenent of the covariates. If the number of reference taxa is less than ‘nRef’, the algorithm will randomly pick extra reference taxa to make up ‘nRef’. The default is NULL since the algorithm will pick reference taxa randomly.
adjust_method The adjusting method used for p value adjustment. Default is “BY” for dependent FDR adjustment. It can take any adjustment method for p.adjust function in R.
fdrRate: The false discovery rate for identifying taxa/OTU/ASV associated with testCov. Default is 0.15.
paraJobs: If sequentialRun is FALSE, this specifies the number of parallel jobs that will be registered to run the algorithm. If specified as NULL, it will automatically detect the cores to decide the number of parallel jobs. Default is NULL.
bootB: Number of bootstrap samples for obtaining confidence interval of estimates in phase 2 for the high dimensional regression. The default is 500.
standardize This takes a logical value TRUE or FALSE. If TRUE, the design matrix for X will be standardized in the analyses and the results. Default is FALSE.
sequentialRun: This takes a logical value TRUE or FALSE. Default is FALSE. This argument could be useful for debug.
refReadsThresh: The threshold of proportion of non-zero sequencing reads for choosing the reference taxon in phase 2. The default is 0.2 which means at least 20% non-zero sequencing reads.
taxDropThresh: The threshold of number of non-zero sequencing reads for each taxon to be dropped from the analysis. The default is 0 which means taxon without any sequencing reads will be dropped from the analysis.
SDThresh: The threshold of standard deviations of sequencing reads for been chosen as the reference taxon in phase 2. The default is 0.05 which means the standard deviation of sequencing reads should be at least 0.05 in order to be chosen as reference taxon.
SDquantilThresh: The threshold of the quantile of standard deviation of sequencing reads, above which could be selected as reference taxon. The default is 0.
balanceCut: The threshold of the proportion of non-zero sequencing reads in each group of a binary variable for choosing the final reference taxa in phase 2. The default number is 0.2 which means at least 20% non-zero sequencing reads in each group are needed to be eligible for being chosen as a final reference taxon.
seed: Random seed for reproducibility. Default is 1. It can be set to be NULL to remove seeding.

Output for IFAA() function

The estimation results are saved in the following lists:

sig_results: A list containing estimating results that are statistically significant.
full_results: A list containing all estimating results. NA denotes unestimable.

The covariates data used in the analyses including testCov and ctrlCov is saved in the following object:

covariatesData: A dataset containing covariates and confounders used in the analyses

Examples

The example datasets dataM and dataC are included in the package. They could be accessed by:

library(IFAA)

data(dataM)
dim(dataM)
#> [1] 40 61
dataM[1:5, 1:8]
#>   id rawCount1 rawCount2 rawCount3 rawCount4 rawCount5 rawCount6 rawCount7
#> 1  1         4        49         2         0       360       222         4
#> 2  2         0        20        14         0        86       211         5
#> 3  3         3         0         3         7         0        57         0
#> 4  4         9        18         5        31        42        58         8
#> 5  5         0         2         1        19        15        67         6

data(dataC)
dim(dataC)
#> [1] 40  4
dataC[1:3, ]
#>   id        v1        v2        v3
#> 1  1  58.06969 -49.90376 -15.30643
#> 2  2  25.96522 -68.58894 -23.10992
#> 3  3 193.71625 124.40186 119.56747

Both the microbiome data dataM and the covariates data dataC contain 40 samples (i.e., 40 rows).

dataM contains 60 taxa with absolute abundances and these are gut microbiome.
dataC contains 3 covariates.

Next we analyze the data to test the association between microbiome and the variable "v1" while adjusting for the variables (potential confounders) "v2" and "v3".

results <- IFAA(MicrobData = dataM,
                CovData = dataC,
                linkIDname = "id",
                testCov = c("v1"),
                ctrlCov = c("v2","v3"),
                fdrRate = 0.15)
#> Data dimensions (after removing missing data if any):
#> 40 samples
#> 60 taxa/OTU/ASV
#> 1 testCov variables in the analysis
#> These are the testCov variables:
#> v1
#> 2 ctrlCov variables in the analysis
#> These are the ctrlCov variables:
#> v2, v3
#> 0 binary covariates in the analysis
#> 25.71 percent of microbiome sequencing reads are zero
#> Start Phase 1 analysis
#> 6 parallel jobs are registered for analyzing 40 reference taxa in Phase 1
#> 33 percent of phase 1 analysis has been done
#> 6 parallel jobs are registered for analyzing 20 reference taxa in Phase 1
#> 67 percent of phase 1 analysis has been done
#> 6 parallel jobs are registered for analyzing 20 reference taxa in Phase 1
#> 100 percent of phase 1 analysis has been done
#> Phase 1 analysis used 1.02 minutes
#> Start Phase 2 parameter estimation
#> Start estimation for the 1th final reference taxon
#> Estimation done for the 1th final reference taxon and it took 0.01 minutes
#> Start estimation for the 2th final reference taxon
#> Estimation done for the 2th final reference taxon and it took 0.009 minutes
#> Phase 2 parameter estimation done and took 0.019 minutes.
#> The entire analysis took 1.04 minutes

In this example, we are only interested in testing the associations with "v1" which is why testCov=c("v1"). The variables "v2" and "v3" are adjusted as potential confounders in the analyses. The final analysis results are saved in the list sig_results:

results$sig_results
#> $v1
#>              estimate      SE est     CI low      CI up  adj p-value
#> rawCount18 0.02223674 0.005107266 0.01222649 0.03224698 1.201099e-03
#> rawCount36 0.02843518 0.005403042 0.01784522 0.03902514 2.926016e-05
#> rawCount41 0.02598367 0.005012267 0.01615963 0.03580772 2.926016e-05

The results found three taxa "rawCount18", "rawCount36", "rawCount41" associated with "v1" while adjusting for "v2" and "v3". The regression coefficients and their 95% confidence intervals are provided. These coefficients correspond to \(\beta^k\) in the model equation.

The interpretation is that

Every unit increase in "v1" is associated with approximately 2.5% increase in the absolute abundance of "rawCount18", approximately 2.6% increase in the absolute abundance of "rawCount36", and approximately 3.0% increase in the absolute abundance of "rawCount41" in the entire gut ecosystem.

All the analyzed covariates including testCov and ctrlCov can be extracted using the object covariatesData. The covariates data of the first 10 subjects can extracted as follows:

results$covariatesData[1:10,]
#>    id         v1         v2          v3
#> 1   1  58.069691  -49.90376  -15.306430
#> 2   2  25.965216  -68.58894  -23.109922
#> 3   3 193.716251  124.40186  119.567468
#> 4   4  72.156467  -98.48536    2.877972
#> 5   5  98.062712   23.55358  -79.893161
#> 6   6  83.094848 -116.95821 -107.641285
#> 7   7   8.217154 -205.64480 -139.958481
#> 8   8  36.169820   58.95708   26.890379
#> 9   9 152.786131  162.60935  138.731954
#> 10 10  41.621790   65.15427   59.974310

MZILN() function

The IFAA package can also implement the Multivariate Zero-Inflated Logistic Normal (MZILN) regression model for estimating and testing the association of abundance ratios with covariates. The MZILN() function estimates and tests the associations of user-specified abundance ratios with covariates. When the denominator taxon of the ratio is independent of the covariates, ‘MZILN()’ should generate similar results as ‘IFAA()’. The regression model of ‘MZILN()’ can be expressed as follows: \[ \log\bigg(\frac{\mathcal{Y}_i^k}{\mathcal{Y}_i^{K+1}}\bigg)|\mathcal{Y}_i^k>0,\mathcal{Y}_i^{K+1}>0=\alpha^{0k}+\mathcal{X}_i^T\alpha^k+\epsilon_i^k,\hspace{0.2cm}k=1,...,K, \] where

\(\mathcal{Y}_i^k\) is the AA of taxa \(k\) in subject \(i\) in the entire ecosystem.
\(\mathcal{Y}_i^{K+1}\) is the reference taxon (specified by user).
\(\mathcal{X}_i\) is the covariate matrix for all covariates including confounders.
\(\alpha^k\) is the regression coefficients that will be estimated and tested.

Input for MZILN() function

Most of the time, users just feed the first six inputs to the function: MicrobData, CovData, linkIDname, targetTaxa, refTaxa and allCov. All other inputs can just take their default values. All the inputs for ‘MZILN()’ are:

MicrobData: Microbiome data matrix containing microbiome absolute abundance or relative abundance with each row per sample and each column per taxon/OTU/ASV (or any other unit). The data matrix can have zero-valued data points. It should also contain an id variable to be linked with the id variable in the covariates data: CovData. This argument can also take file directory path. For example, MicrobData="C://...//microbiomeData.tsv".
CovData: Covariates data matrix containing covariates and confounders with each row per sample and each column per variable. Any categorical variable should be converted into dummy variables in this data matrix unless it can be treated as a continuous variable. It should also contain an id variable to be linked with the id variable in the microbiome data: MicrobData. This argument can also take file directory path. For example, CovData=“C://…//covariatesData.tsv”.
linkIDname The common variable name of the id variable in both MicrobData and CovData. The two data sets will be merged by this id variable.
targetTaxa The numerator taxa names specified by users for the targeted ratios. Default is NULL in which case all taxa are numerator taxa (except the taxa in the argument ‘refTaxa’).
refTaxa Denominator taxa names specified by the user for the targeted ratios. This could be a vector of names.
allCov All covariates of interest (including confounders) for estimating and testing their associations with the targeted ratios. Default is ‘NULL’ meaning that all covariates in covData are of interest.
adjust_method The adjusting method for p value adjustment. Default is “BY” for dependent FDR adjustment. It can take any adjustment method for p.adjust function in R.
fdrRate The false discovery rate for identifying ratios associated with allCov. Default is 0.15.
paraJobs If sequentialRun is FALSE, this specifies the number of parallel jobs that will be registered to run the algorithm. If specified as NULL, it will automatically detect the cores to decide the number of parallel jobs. Default is NULL.
bootB Number of bootstrap samples for obtaining confidence interval of estimates for the high dimensional regression. The default is 500.
taxDropThresh: The threshold of number of non-zero sequencing reads for each taxon to be dropped from the analysis. The default is 0 which means taxon without any sequencing reads will be dropped from the analysis.
standardize This takes a logical value TRUE or FALSE. If TRUE, the design matrix for X will be standardized in the analyses and the results. Default is FALSE.
sequentialRun This takes a logical value TRUE or FALSE. Default is TRUE. It can be set to be “FALSE” to increase speed if there are multiple taxa in the argument ‘refTaxa’.
seed Random seed for reproducibility. Default is 1. It can be set to be NULL to remove seeding.

Output for MZILN() function

The estimation results are saved in the following lists:

targettaxa_result_list: A list containing estimating results for targeted ratios. Only available when targetTaxa is non-empty.
sig_results: A list containing estimating results for all significant ratios

All covariates data used in the analysis is saved in the following object:

covariatesData: A dataset containing all covariates used in the analyses

Examples

We use the same example data The example dataset as that for illustrating the IFAA function. dataM and dataC are included in the package. They could be accessed by:

data(dataM)
dim(dataM)
#> [1] 40 61
dataM[1:5, 1:8]
#>   id rawCount1 rawCount2 rawCount3 rawCount4 rawCount5 rawCount6 rawCount7
#> 1  1         4        49         2         0       360       222         4
#> 2  2         0        20        14         0        86       211         5
#> 3  3         3         0         3         7         0        57         0
#> 4  4         9        18         5        31        42        58         8
#> 5  5         0         2         1        19        15        67         6

data(dataC)
dim(dataC)
#> [1] 40  4
dataC[1:3, ]
#>   id        v1        v2        v3
#> 1  1  58.06969 -49.90376 -15.30643
#> 2  2  25.96522 -68.58894 -23.10992
#> 3  3 193.71625 124.40186 119.56747

Both the microbiome data dataM and the covariates data dataC contain 40 samples (i.e., 40 rows).

dataM contains 60 taxa with absolute abundances and these are gut microbiome.
dataC contains 3 covariates.

Next we analyze the data to test the associations between the ratio “rawCount18/rawCount11” and all the three variables "v1", "v2" and "v3" in a multivariate model where all "v1", "v2" and "v3" are independent variables simultaneously.

results <- MZILN(MicrobData = dataM,
                CovData = dataC,
                 linkIDname = "id",
                 targetTaxa = "rawCount18",
                 refTaxa=c("rawCount11"),
                 allCov=c("v1","v2","v3"),
                 fdrRate=0.15)
#> Data dimensions (after removing missing data if any):
#> 40 samples
#> 60 taxa/OTU/ASV
#> 3 testCov variables in the analysis
#> These are the testCov variables:
#> v1, v2, v3
#> 0 ctrlCov variables in the analysis
#> 0 binary covariates in the analysis
#> 25.71 percent of microbiome sequencing reads are zero
#> Estimation done for the 1th denominator taxon: rawCount11 and it took 0.01 minutes
#> The entire analysis took 0.01 minutes

The final analysis results are saved in the list targettaxa_result_list:

results$targettaxa_result_list
#> $rawCount11
#> $rawCount11$v1
#>              estimate      SE est     CI low      CI up adj p-value
#> rawCount18 0.02310369 0.005570789 0.01218495 0.03402244 0.003085391
#> 
#> $rawCount11$v2
#>               estimate      SE est       CI low       CI up adj p-value
#> rawCount18 0.002604117 0.003173695 -0.003616325 0.008824558           1
#> 
#> $rawCount11$v3
#>                estimate      SE est      CI low        CI up adj p-value
#> rawCount18 -0.006250528 0.002814316 -0.01176659 -0.000734468   0.8055964

The regression coefficients and their 95% confidence intervals are provided. These coefficients correspond to \(\alpha^k\) in the model equation, and can be interpreted as the associations between the covariates and log-ratio of "rawCount18" over ‘“rawCount11”’.

The interpretation for the results is that

Every unit increase in "v1" is associated with approximately 2.3% increase in the abundance ratio of "rawCount18" over "rawCount11" (while controlling for "v2" and "v3"); Every unit increase in "v2" is associated with approximately 0.26% increase in the abundance ratio of "rawCount18" over "rawCount11" (while controlling for "v1" and "v3"), but not statistically significant; Every unit increase in "v3" is associated with approximately -0.63% decrease in the abundance ratio of "rawCount18" over "rawCount11" (while controlling for "v1" and "v2"), but not statistically significant.

We can also extract all the ratios (with "rawCount11" being the denominator taxon) that are significantly associated with any of the covariates as follows:

results$sig_results
#> $rawCount11
#> $rawCount11$v1
#>              estimate      SE est     CI low      CI up  adj p-value
#> rawCount18 0.02310369 0.005570789 0.01218495 0.03402244 0.0030853909
#> rawCount36 0.02965713 0.005894748 0.01810342 0.04121084 0.0001341658
#> rawCount41 0.02562728 0.005462932 0.01491993 0.03633463 0.0003737775

The interpretation for the results is that

Every unit increase in "v1" is associated with approximately 2.3% increase in the abundance ratio of "rawCount18" over "rawCount11" (while controlling for "v2" and "v3"), and it is statistically significant; Every unit increase in "v1" is also associated with approximately 3.0% increase in the abundance ratio of "rawCount36" over "rawCount11" (while controlling for "v2" and "v3"), and it is statistically significant; Every unit increase in "v1" is also associated with approximately 2.6% decrease in the abundance ratio of "rawCount41" over "rawCount11" (while controlling for "v2" and "v3"), and it is statistically significant.

All covariates used in the analysis can be extracted using the object covariatesData. The covariates data of the first 10 subjects are extracted as follows:

results$covariatesData[1:10,]
#>    id         v1         v2          v3
#> 1   1  58.069691  -49.90376  -15.306430
#> 2   2  25.965216  -68.58894  -23.109922
#> 3   3 193.716251  124.40186  119.567468
#> 4   4  72.156467  -98.48536    2.877972
#> 5   5  98.062712   23.55358  -79.893161
#> 6   6  83.094848 -116.95821 -107.641285
#> 7   7   8.217154 -205.64480 -139.958481
#> 8   8  36.169820   58.95708   26.890379
#> 9   9 152.786131  162.60935  138.731954
#> 10 10  41.621790   65.15427   59.974310