cfToolsData 1.0.0
The cfToolsData package provides two pre-trained deep neural network (DNN) models for the cfSort() function in cfTools.
## DNN1
## "/home/biocbuild/.cache/R/ExperimentHub/12e3f36274d64f_8476"
## DNN2
## "/home/biocbuild/.cache/R/ExperimentHub/12e3f33d0cac34_8477"Users can locate the data file at the specified output file path.
It also provides the shape parameters of beta distribution characterizing methylation markers associated with four cancer types for the CancerDetector() function in cfTools.
tumorMarkerParams <- c(
COAD.tumorMarkerParams.hg19(),
LIHC.tumorMarkerParams.hg19(),
LUNG.tumorMarkerParams.hg19(),
STAD.tumorMarkerParams.hg19()
)
names(tumorMarkerParams) <- c(
"COAD.tumorMarkerParams",
"LIHC.tumorMarkerParams",
"LUNG.tumorMarkerParams",
"STAD.tumorMarkerParams"
)
tumorMarkerParams## COAD.tumorMarkerParams
## "/home/biocbuild/.cache/R/ExperimentHub/12e3f329508765_8470"
## LIHC.tumorMarkerParams
## "/home/biocbuild/.cache/R/ExperimentHub/12e3f35e161470_8471"
## LUNG.tumorMarkerParams
## "/home/biocbuild/.cache/R/ExperimentHub/12e3f319da0c01_8472"
## STAD.tumorMarkerParams
## "/home/biocbuild/.cache/R/ExperimentHub/12e3f311b3f28c_8473"Additionally, it includes the shape parameters of beta distribution characterizing methylation markers specific to 29 primary human tissue types for the cfDeconvolve() function in cfTools, as well as the annotations of these markers.
## EH8415
## "/home/biocbuild/.cache/R/ExperimentHub/12e3f36481c60e_8474"## EH8416
## "/home/biocbuild/.cache/R/ExperimentHub/12e3f355877727_8475"## R version 4.3.1 (2023-06-16)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.3 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.18-bioc/R/lib/libRblas.so
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_GB 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: America/New_York
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] cfToolsData_1.0.0 BiocStyle_2.30.0
##
## loaded via a namespace (and not attached):
## [1] KEGGREST_1.42.0 xfun_0.40
## [3] bslib_0.5.1 Biobase_2.62.0
## [5] bitops_1.0-7 vctrs_0.6.4
## [7] tools_4.3.1 generics_0.1.3
## [9] stats4_4.3.1 curl_5.1.0
## [11] tibble_3.2.1 fansi_1.0.5
## [13] AnnotationDbi_1.64.0 RSQLite_2.3.1
## [15] blob_1.2.4 pkgconfig_2.0.3
## [17] dbplyr_2.3.4 S4Vectors_0.40.0
## [19] GenomeInfoDbData_1.2.11 lifecycle_1.0.3
## [21] compiler_4.3.1 Biostrings_2.70.1
## [23] GenomeInfoDb_1.38.0 httpuv_1.6.12
## [25] htmltools_0.5.6.1 sass_0.4.7
## [27] RCurl_1.98-1.12 yaml_2.3.7
## [29] interactiveDisplayBase_1.40.0 pillar_1.9.0
## [31] later_1.3.1 crayon_1.5.2
## [33] jquerylib_0.1.4 ellipsis_0.3.2
## [35] cachem_1.0.8 mime_0.12
## [37] ExperimentHub_2.10.0 AnnotationHub_3.10.0
## [39] tidyselect_1.2.0 digest_0.6.33
## [41] purrr_1.0.2 dplyr_1.1.3
## [43] bookdown_0.36 BiocVersion_3.18.0
## [45] fastmap_1.1.1 cli_3.6.1
## [47] magrittr_2.0.3 utf8_1.2.4
## [49] withr_2.5.1 filelock_1.0.2
## [51] promises_1.2.1 rappdirs_0.3.3
## [53] bit64_4.0.5 rmarkdown_2.25
## [55] XVector_0.42.0 httr_1.4.7
## [57] bit_4.0.5 png_0.1-8
## [59] memoise_2.0.1 shiny_1.7.5.1
## [61] evaluate_0.22 knitr_1.44
## [63] IRanges_2.36.0 BiocFileCache_2.10.0
## [65] rlang_1.1.1 Rcpp_1.0.11
## [67] xtable_1.8-4 glue_1.6.2
## [69] DBI_1.1.3 BiocManager_1.30.22
## [71] BiocGenerics_0.48.0 jsonlite_1.8.7
## [73] R6_2.5.1 zlibbioc_1.48.0