QuickStart
Installation
Data Analyses
Gene expression.
Here is how we can process real data. First we prepare the data set from tximportdata package
require(GenomicRanges)
#> Loading required package: GenomicRanges
#> Loading required package: stats4
#> Loading required package: BiocGenerics
#> Loading required package: generics
#>
#> Attaching package: 'generics'
#> The following objects are masked from 'package:base':
#>
#> as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
#> setequal, union
#>
#> Attaching package: 'BiocGenerics'
#> The following objects are masked from 'package:stats':
#>
#> IQR, mad, sd, var, xtabs
#> The following objects are masked from 'package:base':
#>
#> Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
#> as.data.frame, basename, cbind, colnames, dirname, do.call,
#> duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
#> mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
#> rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
#> unsplit, which.max, which.min
#> Loading required package: S4Vectors
#>
#> Attaching package: 'S4Vectors'
#> The following object is masked from 'package:utils':
#>
#> findMatches
#> The following objects are masked from 'package:base':
#>
#> I, expand.grid, unname
#> Loading required package: IRanges
#> Loading required package: GenomeInfoDb
require(rTensor)
#> Loading required package: rTensor
#>
#> Attaching package: 'rTensor'
#> The following object is masked from 'package:S4Vectors':
#>
#> fold
library("readr")
library("tximport")
library("tximportData")
dir <- system.file("extdata", package="tximportData")
samples <- read.table(file.path(dir,"samples.txt"), header=TRUE)
samples$condition <- factor(rep(c("A","B"),each=3))
rownames(samples) <- samples$run
samples[,c("pop","center","run","condition")]
#> pop center run condition
#> ERR188297 TSI UNIGE ERR188297 A
#> ERR188088 TSI UNIGE ERR188088 A
#> ERR188329 TSI UNIGE ERR188329 A
#> ERR188288 TSI UNIGE ERR188288 B
#> ERR188021 TSI UNIGE ERR188021 B
#> ERR188356 TSI UNIGE ERR188356 B
files <- file.path(dir,"salmon", samples$run, "quant.sf.gz")
names(files) <- samples$run
tx2gene <- read_csv(file.path(dir, "tx2gene.gencode.v27.csv"))
#> Rows: 200401 Columns: 2
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: ","
#> chr (2): TXNAME, GENEID
#>
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
txi <- tximport(files, type="salmon", tx2gene=tx2gene)
#> reading in files with read_tsv
#> 1 2 3 4 5 6
#> summarizing abundance
#> summarizing counts
#> summarizing lengthAs can be seen on the above, this data set is composed of six samples, which are divided into two classes, each of which includes three out of six samples. The number of features is 58288
which is too many to execute small desktops, we reduce number of features to 10,000
Then we reformat count data, txi$counts, as a tensor, Z, whose dimension is 10000 × 3 × 2 and HOSVD was applied to Z to get tensor decomposition using function computeHosvd.
Z <- PrepareSummarizedExperimentTensor(matrix(samples$sample,c(3,2)),
rownames(txi$abundance),array(txi$counts,c(dim(txi$counts)[1],3,2)))
dim(attr(Z,"value"))
#> [1] 10000 3 2
HOSVD <- computeHosvd(Z)
#> | | | 0% | |======================= | 33% | |=============================================== | 67% | |======================================================================| 100%Here 3 and 2 stand for the number of samples in each class and the number of classes, respectively. HOSVD includes output from HOSVD. Next, we need to decide which singular value vectors are used for the download analysis interactively. Since vignettes has no ability to store the output from interactive output from R, you have to input here as
in batch mode. Then you get the above graphic. In actual usage you can
activate interactive mode as
input_all <- selectSingularValueVectorSmall(HOSVD)In interactive mode, you can see “Next”, “Prev” and “Select” radio buttons by which you can select singular value vectors one by one interactively. Now 1 and 2 is entered in input_all, since these correspond to constant among three samples (AAA or BBB) and distinction between A and B, respectively.
Then we try to select features.
We get the above graphic. The left one represents the dependence of
“flatness” of histogram of P-values computed with assuming the
null hypothesis. More or less it can select smallest value. Thus it is
successful. The right one represents the histogram of 1-P-values. Peak at right end
corresponds to genes selected (The peak at the left end does not have
any meaning since they corresponds to P ≃ 1). Then we try to see top
ranked features
head(tableFeatures(Z,index))
#> Feature p value adjusted p value
#> 11 ENSG00000008988.9 0 0
#> 40 ENSG00000044574.7 0 0
#> 89 ENSG00000075618.17 0 0
#> 90 ENSG00000075624.13 0 0
#> 104 ENSG00000080824.18 0 0
#> 118 ENSG00000086758.15 0 0These are associated with P = 0. Thus, successful.
Multiomics data analysis
Next we try to see how we can make use of TDbasedUFE to perform multiomics analyses. In order that, we prepare data set using MOFAdata package as follows.
require(MOFAdata)
#> Loading required package: MOFAdata
data("CLL_data")
data("CLL_covariates")
help(CLL_data)CLL_data is composed of four omics data,
- Drugs: viability values in response to 310 different drugs and concentrations
- Methylation: methylation M-values for the 4248 most variable CpG sites
- mRNA: normalized expression values for the 5000 most variable genes
- Mutations: Mutation status for 69 selected genes
each of which was converted to squared matrix (i. e., liner kernel(Taguchi and Turki 2022))and they are bundle as one tensor using PrepareSummarizedExperimentTensorSquare function, to which HOSVD is applied as follows.
Z <- PrepareSummarizedExperimentTensorSquare(
sample=matrix(colnames(CLL_data$Drugs),1),
feature=list(Drugs=rownames(CLL_data$Drugs),
Methylation=rownames(CLL_data$Methylation),
mRNA=rownames(CLL_data$mRNA),Mutations=rownames(CLL_data$Mutations)),
value=convertSquare(CLL_data),sampleData=list(CLL_covariates[,1]))
HOSVD <- computeHosvdSqure(Z)
#> | | | 0% | |======================= | 33% | |=============================================== | 67% | |======================================================================| 100%CLL_covariate is labeling information, among which we employed the distinction between male (m) and female (f).
table(CLL_covariates[,1])
#>
#> f m
#> 79 121
cond <- list(attr(Z,"sampleData")[[1]],attr(Z,"sampleData")[[1]],seq_len(4))Since a tensor is a bundle of liner kernel, the first two singular value vectors are dedicated to samples and the third (last) one is dedicated to four omics classes (Drugs, Methylation, mRNA and mutations). In order to select which singular value vectors are employed, we execute selectFeatureSquare function in batch mode as follows
In actual usage you can activate interactive mode as
input_all <- selectSingularValueVectorLarge(HOSVD,cond)and can select the eight singular value vetor for samples that represents distinction between male and female and the first singular value vectors to four omics categories that represents the commoness between four omics data (i.e., constant values for four omics data).
Now we come to the stage to select features. Since there are four features, we need to optimize SD for each of them. Try to execute selectFeatureSquare in a batch mode as follows.
index <- selectFeatureSquare(HOSVD,input_all,CLL_data,
de=c(0.3,0.03,0.1,0.1),interact=FALSE) #for batch mode
In actual usage, you can activate interctive mode
index <- selectFeatureSquare(HOSVD,input_all,CLL_data,
de=c(0.3,0.03,0.1,0.1))to see these plots one by one if you hope. In the above, de=c(0.3,0.03,0.1,0.1) represents initial SD for the optimization of SD for each of four omics. There might be need for some trial & errors to get good initial values. Every time you type enter in an interactive mode, you can see one of four plots for four omics data.
Now the output includes four lists each of which corresponds to one of four omics data. Each list is composed of two vectors whose length is equivalent to the number of features in each of omics data. Two vectors, index and p.value, stores logical vector that shows if individual features are selected and raw P-values.
In order to see selected features for all four omics data, tableFeatureSquare function must be repeated four times as
for (id in seq_len(4)){print(head(tableFeaturesSquare(Z,index,id)))}
#> [1] Feature p value adjusted p value
#> <0 rows> (or 0-length row.names)
#> [1] Feature p value adjusted p value
#> <0 rows> (or 0-length row.names)
#> Feature p value adjusted p value
#> 4 ENSG00000152953 9.669707e-13 4.834854e-09
#> 3 ENSG00000163873 1.369068e-10 3.422671e-07
#> 7 ENSG00000169398 2.841302e-09 4.735504e-06
#> 2 ENSG00000095777 3.955241e-09 4.944052e-06
#> 9 ENSG00000180287 9.636882e-08 9.636882e-05
#> 11 ENSG00000186567 2.325751e-07 1.938126e-04
#> Feature p value adjusted p value
#> 1 del11q22.3 3.499307e-24 2.414522e-22
#> 6 SF3B1 1.334788e-15 4.605018e-14
#> 3 del13q14_any 9.427628e-10 2.168355e-08
#> 5 NOTCH1 3.071643e-09 5.298584e-08
#> 7 IGHV 4.023699e-07 5.552704e-06
#> 4 del17p13 9.697530e-06 1.115216e-04Conclusion
In this vignettes, we briefly introduce how we can make use of TDbasedUFE to perform gene expression analysis and multiomics analysis. I am glad if you can make use of it as well for your own research.
sessionInfo()
#> 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] stats4 stats graphics grDevices utils datasets methods
#> [8] base
#>
#> other attached packages:
#> [1] MOFAdata_1.22.0 tximportData_1.34.0 tximport_1.35.0
#> [4] readr_2.1.5 rTensor_1.4.8 GenomicRanges_1.59.1
#> [7] GenomeInfoDb_1.43.1 IRanges_2.41.1 S4Vectors_0.45.2
#> [10] BiocGenerics_0.53.3 generics_0.1.3 TDbasedUFE_1.7.0
#> [13] BiocStyle_2.35.0
#>
#> loaded via a namespace (and not attached):
#> [1] sass_0.4.9 utf8_1.2.4 hms_1.1.3
#> [4] digest_0.6.37 magrittr_2.0.3 evaluate_1.0.1
#> [7] fastmap_1.2.0 jsonlite_1.8.9 promises_1.3.0
#> [10] BiocManager_1.30.25 httr_1.4.7 fansi_1.0.6
#> [13] UCSC.utils_1.3.0 jquerylib_0.1.4 cli_3.6.3
#> [16] shiny_1.9.1 crayon_1.5.3 rlang_1.1.4
#> [19] XVector_0.47.0 bit64_4.5.2 cachem_1.1.0
#> [22] yaml_2.3.10 parallel_4.4.2 tools_4.4.2
#> [25] tzdb_0.4.0 httpuv_1.6.15 GenomeInfoDbData_1.2.13
#> [28] mime_0.12 buildtools_1.0.0 vctrs_0.6.5
#> [31] R6_2.5.1 lifecycle_1.0.4 zlibbioc_1.52.0
#> [34] bit_4.5.0 vroom_1.6.5 pkgconfig_2.0.3
#> [37] later_1.3.2 pillar_1.9.0 bslib_0.8.0
#> [40] glue_1.8.0 Rcpp_1.0.13-1 tidyselect_1.2.1
#> [43] xfun_0.49 tibble_3.2.1 sys_3.4.3
#> [46] knitr_1.49 xtable_1.8-4 htmltools_0.5.8.1
#> [49] rmarkdown_2.29 maketools_1.3.1 compiler_4.4.2