Description
Tensor Composition Analysis (TCA) allows the deconvolution of two-dimensional data (features by observations) coming from a mixture of heterogeneous sources into a three-dimensional matrix of signals (features by observations by sources). The TCA framework further allows to test the features in the data for different statistical relations with an outcome of interest while modeling source-specific effects; particularly, it allows to look for statistical relations between source-specific signals and an outcome. For example, TCA can deconvolve bulk tissue-level DNA methylation data (methylation sites by individuals) into a three-dimensional tensor of cell-type-specific methylation levels for each individual (i.e. methylation sites by individuals by cell types) and it allows to detect cell-type-specific statistical relations (associations) with phenotypes. For more details see Rahmani et al. (2019) <DOI:10.1038/s41467-019-11052-9>.
Downloads
274
Last 30 days
11523rd
274
Last 90 days
274
Last year
CRAN Check Status
14
NOTE
Show all 14 flavors
| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | NOTE |
| r-devel-linux-x86_64-debian-gcc | NOTE |
| r-devel-linux-x86_64-fedora-clang | NOTE |
| r-devel-linux-x86_64-fedora-gcc | NOTE |
| r-devel-macos-arm64 | NOTE |
| r-devel-windows-x86_64 | NOTE |
| r-oldrel-macos-arm64 | NOTE |
| r-oldrel-macos-x86_64 | NOTE |
| r-oldrel-windows-x86_64 | NOTE |
| r-patched-linux-x86_64 | NOTE |
| r-release-linux-x86_64 | NOTE |
| r-release-macos-arm64 | NOTE |
| r-release-macos-x86_64 | NOTE |
| r-release-windows-x86_64 | NOTE |
Check details (21 non-OK)
NOTE
r-devel-linux-x86_64-debian-clang
CRAN incoming feasibility
Maintainer: ‘Elior Rahmani <elior.rahmani@gmail.com>’ Package CITATION file contains call(s) to old-style personList() or as.personList(). Please use c() on person objects instead. Package CITATION file contains call(s) to old-style citEntry(). Please use bibentry() instead.
NOTE
r-devel-linux-x86_64-debian-clang
Rd files
checkRd: (-1) tca.Rd:35: Lost braces; missing escapes or markup?
35 | \item{C1.map}{An \code{p1} by \code{k} matrix of 0/1 values, indicating for each of the \code{p1} covariates in \code{C1} whether to consider its potential effects on the values of each of the \code{k} sources (e.g., if position \code{i,j} in \code{C1.map} is 1 then the potential effect of the \code{i}-th covariate in \code{C1} on the {j}-th source will be considered). If \code{C1.map == NULL} then effects for all covariates in \code{C1} will be considered in each of the sources. Note that \code{C1.map} is available only if \code{constrain_mu == TRUE}.}
| ^
NOTE
r-devel-linux-x86_64-debian-gcc
CRAN incoming feasibility
Maintainer: ‘Elior Rahmani <elior.rahmani@gmail.com>’ Package CITATION file contains call(s) to old-style personList() or as.personList(). Please use c() on person objects instead. Package CITATION file contains call(s) to old-style citEntry(). Please use bibentry() instead.
NOTE
r-devel-linux-x86_64-debian-gcc
Rd files
checkRd: (-1) tca.Rd:35: Lost braces; missing escapes or markup?
35 | \item{C1.map}{An \code{p1} by \code{k} matrix of 0/1 values, indicating for each of the \code{p1} covariates in \code{C1} whether to consider its potential effects on the values of each of the \code{k} sources (e.g., if position \code{i,j} in \code{C1.map} is 1 then the potential effect of the \code{i}-th covariate in \code{C1} on the {j}-th source will be considered). If \code{C1.map == NULL} then effects for all covariates in \code{C1} will be considered in each of the sources. Note that \code{C1.map} is available only if \code{constrain_mu == TRUE}.}
| ^
NOTE
r-devel-linux-x86_64-fedora-clang
Rd files
checkRd: (-1) tca.Rd:35: Lost braces; missing escapes or markup?
35 | \item{C1.map}{An \code{p1} by \code{k} matrix of 0/1 values, indicating for each of the \code{p1} covariates in \code{C1} whether to consider its potential effects on the values of each of the \code{k} sources (e.g., if position \code{i,j} in \code{C1.map} is 1 then the potential effect of the \code{i}-th covariate in \code{C1} on the {j}-th source will be considered). If \code{C1.map == NULL} then effects for all covariates in \code{C1} will be considered in each of the sources. Note that \code{C1.map} is available only if \code{constrain_mu == TRUE}.}
| ^
NOTE
r-devel-linux-x86_64-fedora-clang
dependencies in R code
Namespaces in Imports field not imported from: ‘Matrix’ ‘quadprog’ All declared Imports should be used.
NOTE
r-devel-linux-x86_64-fedora-gcc
Rd files
checkRd: (-1) tca.Rd:35: Lost braces; missing escapes or markup?
35 | \item{C1.map}{An \code{p1} by \code{k} matrix of 0/1 values, indicating for each of the \code{p1} covariates in \code{C1} whether to consider its potential effects on the values of each of the \code{k} sources (e.g., if position \code{i,j} in \code{C1.map} is 1 then the potential effect of the \code{i}-th covariate in \code{C1} on the {j}-th source will be considered). If \code{C1.map == NULL} then effects for all covariates in \code{C1} will be considered in each of the sources. Note that \code{C1.map} is available only if \code{constrain_mu == TRUE}.}
| ^
NOTE
r-devel-linux-x86_64-fedora-gcc
dependencies in R code
Namespaces in Imports field not imported from: ‘Matrix’ ‘quadprog’ All declared Imports should be used.
NOTE
r-devel-macos-arm64
Rd files
checkRd: (-1) tca.Rd:35: Lost braces; missing escapes or markup?
35 | \item{C1.map}{An \code{p1} by \code{k} matrix of 0/1 values, indicating for each of the \code{p1} covariates in \code{C1} whether to consider its potential effects on the values of each of the \code{k} sources (e.g., if position \code{i,j} in \code{C1.map} is 1 then the potential effect of the \code{i}-th covariate in \code{C1} on the {j}-th source will be considered). If \code{C1.map == NULL} then effects for all covariates in \code{C1} will be considered in each of the sources. Note that \code{C1.map} is available only if \code{constrain_mu == TRUE}.}
| ^
NOTE
r-devel-windows-x86_64
Rd files
checkRd: (-1) tca.Rd:35: Lost braces; missing escapes or markup?
35 | \item{C1.map}{An \code{p1} by \code{k} matrix of 0/1 values, indicating for each of the \code{p1} covariates in \code{C1} whether to consider its potential effects on the values of each of the \code{k} sources (e.g., if position \code{i,j} in \code{C1.map} is 1 then the potential effect of the \code{i}-th covariate in \code{C1} on the {j}-th source will be considered). If \code{C1.map == NULL} then effects for all covariates in \code{C1} will be considered in each of the sources. Note that \code{C1.map} is available only if \code{constrain_mu == TRUE}.}
| ^
NOTE
r-oldrel-macos-arm64
LazyData
'LazyData' is specified without a 'data' directory
NOTE
r-oldrel-macos-arm64
Rd files
checkRd: (-1) tca.Rd:35: Lost braces; missing escapes or markup?
35 | \item{C1.map}{An \code{p1} by \code{k} matrix of 0/1 values, indicating for each of the \code{p1} covariates in \code{C1} whether to consider its potential effects on the values of each of the \code{k} sources (e.g., if position \code{i,j} in \code{C1.map} is 1 then the potential effect of the \code{i}-th covariate in \code{C1} on the {j}-th source will be considered). If \code{C1.map == NULL} then effects for all covariates in \code{C1} will be considered in each of the sources. Note that \code{C1.map} is available only if \code{constrain_mu == TRUE}.}
| ^
NOTE
r-oldrel-macos-x86_64
LazyData
'LazyData' is specified without a 'data' directory
NOTE
r-oldrel-macos-x86_64
Rd files
checkRd: (-1) tca.Rd:35: Lost braces; missing escapes or markup?
35 | \item{C1.map}{An \code{p1} by \code{k} matrix of 0/1 values, indicating for each of the \code{p1} covariates in \code{C1} whether to consider its potential effects on the values of each of the \code{k} sources (e.g., if position \code{i,j} in \code{C1.map} is 1 then the potential effect of the \code{i}-th covariate in \code{C1} on the {j}-th source will be considered). If \code{C1.map == NULL} then effects for all covariates in \code{C1} will be considered in each of the sources. Note that \code{C1.map} is available only if \code{constrain_mu == TRUE}.}
| ^
NOTE
r-oldrel-windows-x86_64
LazyData
'LazyData' is specified without a 'data' directory
NOTE
r-oldrel-windows-x86_64
Rd files
checkRd: (-1) tca.Rd:35: Lost braces; missing escapes or markup?
35 | \item{C1.map}{An \code{p1} by \code{k} matrix of 0/1 values, indicating for each of the \code{p1} covariates in \code{C1} whether to consider its potential effects on the values of each of the \code{k} sources (e.g., if position \code{i,j} in \code{C1.map} is 1 then the potential effect of the \code{i}-th covariate in \code{C1} on the {j}-th source will be considered). If \code{C1.map == NULL} then effects for all covariates in \code{C1} will be considered in each of the sources. Note that \code{C1.map} is available only if \code{constrain_mu == TRUE}.}
| ^
NOTE
r-patched-linux-x86_64
Rd files
checkRd: (-1) tca.Rd:35: Lost braces; missing escapes or markup?
35 | \item{C1.map}{An \code{p1} by \code{k} matrix of 0/1 values, indicating for each of the \code{p1} covariates in \code{C1} whether to consider its potential effects on the values of each of the \code{k} sources (e.g., if position \code{i,j} in \code{C1.map} is 1 then the potential effect of the \code{i}-th covariate in \code{C1} on the {j}-th source will be considered). If \code{C1.map == NULL} then effects for all covariates in \code{C1} will be considered in each of the sources. Note that \code{C1.map} is available only if \code{constrain_mu == TRUE}.}
| ^
NOTE
r-release-linux-x86_64
Rd files
checkRd: (-1) tca.Rd:35: Lost braces; missing escapes or markup?
35 | \item{C1.map}{An \code{p1} by \code{k} matrix of 0/1 values, indicating for each of the \code{p1} covariates in \code{C1} whether to consider its potential effects on the values of each of the \code{k} sources (e.g., if position \code{i,j} in \code{C1.map} is 1 then the potential effect of the \code{i}-th covariate in \code{C1} on the {j}-th source will be considered). If \code{C1.map == NULL} then effects for all covariates in \code{C1} will be considered in each of the sources. Note that \code{C1.map} is available only if \code{constrain_mu == TRUE}.}
| ^
NOTE
r-release-macos-arm64
Rd files
checkRd: (-1) tca.Rd:35: Lost braces; missing escapes or markup?
35 | \item{C1.map}{An \code{p1} by \code{k} matrix of 0/1 values, indicating for each of the \code{p1} covariates in \code{C1} whether to consider its potential effects on the values of each of the \code{k} sources (e.g., if position \code{i,j} in \code{C1.map} is 1 then the potential effect of the \code{i}-th covariate in \code{C1} on the {j}-th source will be considered). If \code{C1.map == NULL} then effects for all covariates in \code{C1} will be considered in each of the sources. Note that \code{C1.map} is available only if \code{constrain_mu == TRUE}.}
| ^
NOTE
r-release-macos-x86_64
Rd files
checkRd: (-1) tca.Rd:35: Lost braces; missing escapes or markup?
35 | \item{C1.map}{An \code{p1} by \code{k} matrix of 0/1 values, indicating for each of the \code{p1} covariates in \code{C1} whether to consider its potential effects on the values of each of the \code{k} sources (e.g., if position \code{i,j} in \code{C1.map} is 1 then the potential effect of the \code{i}-th covariate in \code{C1} on the {j}-th source will be considered). If \code{C1.map == NULL} then effects for all covariates in \code{C1} will be considered in each of the sources. Note that \code{C1.map} is available only if \code{constrain_mu == TRUE}.}
| ^
NOTE
r-release-windows-x86_64
Rd files
checkRd: (-1) tca.Rd:35: Lost braces; missing escapes or markup?
35 | \item{C1.map}{An \code{p1} by \code{k} matrix of 0/1 values, indicating for each of the \code{p1} covariates in \code{C1} whether to consider its potential effects on the values of each of the \code{k} sources (e.g., if position \code{i,j} in \code{C1.map} is 1 then the potential effect of the \code{i}-th covariate in \code{C1} on the {j}-th source will be considered). If \code{C1.map == NULL} then effects for all covariates in \code{C1} will be considered in each of the sources. Note that \code{C1.map} is available only if \code{constrain_mu == TRUE}.}
| ^
Check History
NOTE 0 OK · 14 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 9, 2026
NOTE
r-devel-linux-x86_64-debian-clang
CRAN incoming feasibility
Maintainer: ‘Elior Rahmani <elior.rahmani@gmail.com>’ Package CITATION file contains call(s) to old-style personList() or as.personList(). Please use c() on person objects instead. Package CITATION file contains call(s) to old-style citEntry(). Please use bibentry() instead.
NOTE
r-devel-linux-x86_64-debian-gcc
CRAN incoming feasibility
Maintainer: ‘Elior Rahmani <elior.rahmani@gmail.com>’ Package CITATION file contains call(s) to old-style personList() or as.personList(). Please use c() on person objects instead. Package CITATION file contains call(s) to old-style citEntry(). Please use bibentry() instead.
NOTE
r-devel-linux-x86_64-fedora-clang
dependencies in R code
Namespaces in Imports field not imported from: ‘Matrix’ ‘quadprog’ All declared Imports should be used.
NOTE
r-devel-linux-x86_64-fedora-gcc
dependencies in R code
Namespaces in Imports field not imported from: ‘Matrix’ ‘quadprog’ All declared Imports should be used.
NOTE
r-devel-macos-arm64
Rd files
checkRd: (-1) tca.Rd:35: Lost braces; missing escapes or markup?
35 | \item{C1.map}{An \code{p1} by \code{k} matrix of 0/1 values, indicating for each of the \code{p1} covariates in \code{C1} whether to consider its potential effects on the values of each of the \code{k} sources (e.g., if position \code{i,j} in \code{C1.map} is 1 then the potential effect of the \code{i}-th covariate in \code{C1} on the {j}-th source will be considered). If \code{C1.map == NULL} then effects for all covariat
NOTE
r-devel-windows-x86_64
Rd files
checkRd: (-1) tca.Rd:35: Lost braces; missing escapes or markup?
35 | \item{C1.map}{An \code{p1} by \code{k} matrix of 0/1 values, indicating for each of the \code{p1} covariates in \code{C1} whether to consider its potential effects on the values of each of the \code{k} sources (e.g., if position \code{i,j} in \code{C1.map} is 1 then the potential effect of the \code{i}-th covariate in \code{C1} on the {j}-th source will be considered). If \code{C1.map == NULL} then effects for all covariat
NOTE
r-patched-linux-x86_64
Rd files
checkRd: (-1) tca.Rd:35: Lost braces; missing escapes or markup?
35 | \item{C1.map}{An \code{p1} by \code{k} matrix of 0/1 values, indicating for each of the \code{p1} covariates in \code{C1} whether to consider its potential effects on the values of each of the \code{k} sources (e.g., if position \code{i,j} in \code{C1.map} is 1 then the potential effect of the \code{i}-th covariate in \code{C1} on the {j}-th source will be considered). If \code{C1.map == NULL} then effects for all covariat
NOTE
r-release-linux-x86_64
Rd files
checkRd: (-1) tca.Rd:35: Lost braces; missing escapes or markup?
35 | \item{C1.map}{An \code{p1} by \code{k} matrix of 0/1 values, indicating for each of the \code{p1} covariates in \code{C1} whether to consider its potential effects on the values of each of the \code{k} sources (e.g., if position \code{i,j} in \code{C1.map} is 1 then the potential effect of the \code{i}-th covariate in \code{C1} on the {j}-th source will be considered). If \code{C1.map == NULL} then effects for all covariat
NOTE
r-release-macos-arm64
Rd files
checkRd: (-1) tca.Rd:35: Lost braces; missing escapes or markup?
35 | \item{C1.map}{An \code{p1} by \code{k} matrix of 0/1 values, indicating for each of the \code{p1} covariates in \code{C1} whether to consider its potential effects on the values of each of the \code{k} sources (e.g., if position \code{i,j} in \code{C1.map} is 1 then the potential effect of the \code{i}-th covariate in \code{C1} on the {j}-th source will be considered). If \code{C1.map == NULL} then effects for all covariat
NOTE
r-release-macos-x86_64
Rd files
checkRd: (-1) tca.Rd:35: Lost braces; missing escapes or markup?
35 | \item{C1.map}{An \code{p1} by \code{k} matrix of 0/1 values, indicating for each of the \code{p1} covariates in \code{C1} whether to consider its potential effects on the values of each of the \code{k} sources (e.g., if position \code{i,j} in \code{C1.map} is 1 then the potential effect of the \code{i}-th covariate in \code{C1} on the {j}-th source will be considered). If \code{C1.map == NULL} then effects for all covariat
NOTE
r-release-windows-x86_64
Rd files
checkRd: (-1) tca.Rd:35: Lost braces; missing escapes or markup?
35 | \item{C1.map}{An \code{p1} by \code{k} matrix of 0/1 values, indicating for each of the \code{p1} covariates in \code{C1} whether to consider its potential effects on the values of each of the \code{k} sources (e.g., if position \code{i,j} in \code{C1.map} is 1 then the potential effect of the \code{i}-th covariate in \code{C1} on the {j}-th source will be considered). If \code{C1.map == NULL} then effects for all covariat
NOTE
r-oldrel-macos-arm64
Rd files
checkRd: (-1) tca.Rd:35: Lost braces; missing escapes or markup?
35 | \item{C1.map}{An \code{p1} by \code{k} matrix of 0/1 values, indicating for each of the \code{p1} covariates in \code{C1} whether to consider its potential effects on the values of each of the \code{k} sources (e.g., if position \code{i,j} in \code{C1.map} is 1 then the potential effect of the \code{i}-th covariate in \code{C1} on the {j}-th source will be considered). If \code{C1.map == NULL} then effects for all covariat
NOTE
r-oldrel-macos-x86_64
Rd files
checkRd: (-1) tca.Rd:35: Lost braces; missing escapes or markup?
35 | \item{C1.map}{An \code{p1} by \code{k} matrix of 0/1 values, indicating for each of the \code{p1} covariates in \code{C1} whether to consider its potential effects on the values of each of the \code{k} sources (e.g., if position \code{i,j} in \code{C1.map} is 1 then the potential effect of the \code{i}-th covariate in \code{C1} on the {j}-th source will be considered). If \code{C1.map == NULL} then effects for all covariat
NOTE
r-oldrel-windows-x86_64
Rd files
checkRd: (-1) tca.Rd:35: Lost braces; missing escapes or markup?
35 | \item{C1.map}{An \code{p1} by \code{k} matrix of 0/1 values, indicating for each of the \code{p1} covariates in \code{C1} whether to consider its potential effects on the values of each of the \code{k} sources (e.g., if position \code{i,j} in \code{C1.map} is 1 then the potential effect of the \code{i}-th covariate in \code{C1} on the {j}-th source will be considered). If \code{C1.map == NULL} then effects for all covariat
Dependency Network
Version History
new
1.2.1
Mar 9, 2026