diff --git a/articles/manipulation.html b/articles/manipulation.html index 91a4015..ce78e3e 100644 --- a/articles/manipulation.html +++ b/articles/manipulation.html @@ -89,7 +89,7 @@

Yagmur yagmur.simsek@hsrw.org -

2024-10-20

+

2024-10-29

Source: vignettes/articles/manipulation.Rmd @@ -365,45 +365,45 @@

Session info## [3] ttservice_0.4.1 tidyr_1.3.1 ## [5] tidySingleCellExperiment_1.15.5 lubridate_1.9.3 ## [7] dplyr_1.1.4 miaTime_0.1.22 -## [9] mia_1.13.44 TreeSummarizedExperiment_2.13.0 +## [9] mia_1.13.47 TreeSummarizedExperiment_2.13.0 ## [11] Biostrings_2.73.2 XVector_0.45.0 ## [13] SingleCellExperiment_1.27.2 MultiAssayExperiment_1.31.5 -## [15] SummarizedExperiment_1.35.2 Biobase_2.65.1 -## [17] GenomicRanges_1.57.1 GenomeInfoDb_1.41.1 +## [15] SummarizedExperiment_1.35.5 Biobase_2.65.1 +## [17] GenomicRanges_1.57.2 GenomeInfoDb_1.41.2 ## [19] IRanges_2.39.2 S4Vectors_0.43.2 -## [21] BiocGenerics_0.51.2 MatrixGenerics_1.17.0 +## [21] BiocGenerics_0.51.3 MatrixGenerics_1.17.1 ## [23] matrixStats_1.4.1 BiocStyle_2.33.1 ## ## loaded via a namespace (and not attached): -## [1] rstudioapi_0.17.0 jsonlite_1.8.9 +## [1] rstudioapi_0.17.1 jsonlite_1.8.9 ## [3] magrittr_2.0.3 ggbeeswarm_0.7.2 ## [5] nloptr_2.1.1 rmarkdown_2.28 -## [7] fs_1.6.4 zlibbioc_1.51.1 +## [7] fs_1.6.4 zlibbioc_1.51.2 ## [9] ragg_1.3.3 vctrs_0.6.5 ## [11] minqa_1.2.8 DelayedMatrixStats_1.27.3 ## [13] base64enc_0.1-3 htmltools_0.5.8.1 -## [15] S4Arrays_1.5.10 BiocNeighbors_1.99.1 -## [17] SparseArray_1.5.41 Formula_1.2-5 +## [15] S4Arrays_1.5.11 BiocNeighbors_1.99.3 +## [17] SparseArray_1.5.45 Formula_1.2-5 ## [19] sass_0.4.9 bslib_0.8.0 ## [21] htmlwidgets_1.6.4 desc_1.4.3 ## [23] sandwich_3.1-1 plyr_1.8.9 -## [25] DECIPHER_3.1.4 plotly_4.10.4 +## [25] DECIPHER_3.1.5 plotly_4.10.4 ## [27] zoo_1.8-12 cachem_1.1.0 -## [29] igraph_2.0.3 lifecycle_1.0.4 +## [29] igraph_2.1.1 lifecycle_1.0.4 ## [31] pkgconfig_2.0.3 rsvd_1.0.5 -## [33] Matrix_1.7-0 R6_2.5.1 +## [33] Matrix_1.7-1 R6_2.5.1 ## [35] fastmap_1.2.0 GenomeInfoDbData_1.2.13 ## [37] digest_0.6.37 colorspace_2.1-1 ## [39] scater_1.33.4 irlba_2.3.5.1 -## [41] textshaping_0.4.0 Hmisc_5.1-3 -## [43] vegan_2.6-8 beachmat_2.21.6 +## [41] textshaping_0.4.0 Hmisc_5.2-0 +## [43] vegan_2.6-8 beachmat_2.21.9 ## [45] timechange_0.3.0 fansi_1.0.6 ## [47] mgcv_1.9-1 httr_1.4.7 ## [49] abind_1.4-8 compiler_4.4.1 -## [51] withr_3.0.1 htmlTable_2.4.3 +## [51] withr_3.0.2 htmlTable_2.4.3 ## [53] backports_1.5.0 BiocParallel_1.39.0 ## [55] viridis_0.6.5 DBI_1.2.3 -## [57] MASS_7.3-61 DelayedArray_0.31.12 +## [57] MASS_7.3-61 DelayedArray_0.31.14 ## [59] bluster_1.15.1 permute_0.9-7 ## [61] tools_4.4.1 vipor_0.4.7 ## [63] foreign_0.8-87 beeswarm_0.4.0 @@ -412,16 +412,16 @@

Session info## [69] grid_4.4.1 checkmate_2.3.2 ## [71] cluster_2.1.6 reshape2_1.4.4 ## [73] lpSolve_5.6.21 generics_0.1.3 -## [75] gtable_0.3.5 mediation_4.5.0 -## [77] data.table_1.16.0 BiocSingular_1.21.4 +## [75] gtable_0.3.6 mediation_4.5.0 +## [77] data.table_1.16.2 BiocSingular_1.21.4 ## [79] ScaledMatrix_1.13.0 utf8_1.2.4 ## [81] ggrepel_0.9.6 pillar_1.9.0 ## [83] stringr_1.5.1 yulab.utils_0.1.7 ## [85] splines_4.4.1 treeio_1.29.1 ## [87] lattice_0.22-6 tidyselect_1.2.1 -## [89] DirichletMultinomial_1.47.0 scuttle_1.15.4 +## [89] DirichletMultinomial_1.47.2 scuttle_1.15.5 ## [91] knitr_1.48 gridExtra_2.3 -## [93] bookdown_0.40 xfun_0.48 +## [93] bookdown_0.41 xfun_0.48 ## [95] rbiom_1.0.3 stringi_1.8.4 ## [97] UCSC.utils_1.1.0 lazyeval_0.2.2 ## [99] yaml_2.3.10 boot_1.3-31 @@ -433,7 +433,7 @@

Session info## [111] Rcpp_1.0.13 parallel_4.4.1 ## [113] ellipsis_0.3.2 pkgdown_2.1.1 ## [115] sparseMatrixStats_1.17.2 lme4_1.1-35.5 -## [117] slam_0.1-53 mvtnorm_1.3-1 +## [117] slam_0.1-54 mvtnorm_1.3-1 ## [119] decontam_1.25.0 viridisLite_0.4.2 ## [121] tidytree_0.4.6 scales_1.3.0 ## [123] purrr_1.0.2 crayon_1.5.3 diff --git a/articles/miaTime.html b/articles/miaTime.html index c38fb60..c3f64f9 100644 --- a/articles/miaTime.html +++ b/articles/miaTime.html @@ -89,7 +89,7 @@

Yagmur -

2024-10-20

+

2024-10-29

Source: vignettes/miaTime.Rmd @@ -145,45 +145,45 @@

Session info## [8] base ## ## other attached packages: -## [1] miaTime_0.1.22 mia_1.13.44 +## [1] miaTime_0.1.22 mia_1.13.47 ## [3] TreeSummarizedExperiment_2.13.0 Biostrings_2.73.2 ## [5] XVector_0.45.0 SingleCellExperiment_1.27.2 -## [7] MultiAssayExperiment_1.31.5 SummarizedExperiment_1.35.2 -## [9] Biobase_2.65.1 GenomicRanges_1.57.1 -## [11] GenomeInfoDb_1.41.1 IRanges_2.39.2 -## [13] S4Vectors_0.43.2 BiocGenerics_0.51.2 -## [15] MatrixGenerics_1.17.0 matrixStats_1.4.1 +## [7] MultiAssayExperiment_1.31.5 SummarizedExperiment_1.35.5 +## [9] Biobase_2.65.1 GenomicRanges_1.57.2 +## [11] GenomeInfoDb_1.41.2 IRanges_2.39.2 +## [13] S4Vectors_0.43.2 BiocGenerics_0.51.3 +## [15] MatrixGenerics_1.17.1 matrixStats_1.4.1 ## [17] BiocStyle_2.33.1 ## ## loaded via a namespace (and not attached): -## [1] rstudioapi_0.17.0 jsonlite_1.8.9 +## [1] rstudioapi_0.17.1 jsonlite_1.8.9 ## [3] magrittr_2.0.3 ggbeeswarm_0.7.2 ## [5] nloptr_2.1.1 rmarkdown_2.28 -## [7] fs_1.6.4 zlibbioc_1.51.1 +## [7] fs_1.6.4 zlibbioc_1.51.2 ## [9] ragg_1.3.3 vctrs_0.6.5 ## [11] minqa_1.2.8 DelayedMatrixStats_1.27.3 ## [13] base64enc_0.1-3 htmltools_0.5.8.1 -## [15] S4Arrays_1.5.10 BiocNeighbors_1.99.1 -## [17] SparseArray_1.5.41 Formula_1.2-5 +## [15] S4Arrays_1.5.11 BiocNeighbors_1.99.3 +## [17] SparseArray_1.5.45 Formula_1.2-5 ## [19] sass_0.4.9 bslib_0.8.0 ## [21] htmlwidgets_1.6.4 desc_1.4.3 ## [23] sandwich_3.1-1 plyr_1.8.9 -## [25] DECIPHER_3.1.4 zoo_1.8-12 -## [27] cachem_1.1.0 igraph_2.0.3 +## [25] DECIPHER_3.1.5 zoo_1.8-12 +## [27] cachem_1.1.0 igraph_2.1.1 ## [29] lifecycle_1.0.4 pkgconfig_2.0.3 -## [31] rsvd_1.0.5 Matrix_1.7-0 +## [31] rsvd_1.0.5 Matrix_1.7-1 ## [33] R6_2.5.1 fastmap_1.2.0 ## [35] GenomeInfoDbData_1.2.13 digest_0.6.37 ## [37] colorspace_2.1-1 scater_1.33.4 ## [39] irlba_2.3.5.1 textshaping_0.4.0 -## [41] Hmisc_5.1-3 vegan_2.6-8 -## [43] beachmat_2.21.6 fansi_1.0.6 +## [41] Hmisc_5.2-0 vegan_2.6-8 +## [43] beachmat_2.21.9 fansi_1.0.6 ## [45] mgcv_1.9-1 httr_1.4.7 ## [47] abind_1.4-8 compiler_4.4.1 ## [49] htmlTable_2.4.3 backports_1.5.0 ## [51] BiocParallel_1.39.0 viridis_0.6.5 ## [53] DBI_1.2.3 MASS_7.3-61 -## [55] DelayedArray_0.31.12 bluster_1.15.1 +## [55] DelayedArray_0.31.14 bluster_1.15.1 ## [57] permute_0.9-7 tools_4.4.1 ## [59] vipor_0.4.7 foreign_0.8-87 ## [61] beeswarm_0.4.0 ape_5.8 @@ -191,17 +191,17 @@

Session info## [65] nlme_3.1-166 grid_4.4.1 ## [67] checkmate_2.3.2 cluster_2.1.6 ## [69] reshape2_1.4.4 lpSolve_5.6.21 -## [71] generics_0.1.3 gtable_0.3.5 +## [71] generics_0.1.3 gtable_0.3.6 ## [73] mediation_4.5.0 tidyr_1.3.1 -## [75] data.table_1.16.0 BiocSingular_1.21.4 +## [75] data.table_1.16.2 BiocSingular_1.21.4 ## [77] ScaledMatrix_1.13.0 utf8_1.2.4 ## [79] ggrepel_0.9.6 pillar_1.9.0 ## [81] stringr_1.5.1 yulab.utils_0.1.7 ## [83] splines_4.4.1 dplyr_1.1.4 ## [85] treeio_1.29.1 lattice_0.22-6 -## [87] tidyselect_1.2.1 DirichletMultinomial_1.47.0 -## [89] scuttle_1.15.4 knitr_1.48 -## [91] gridExtra_2.3 bookdown_0.40 +## [87] tidyselect_1.2.1 DirichletMultinomial_1.47.2 +## [89] scuttle_1.15.5 knitr_1.48 +## [91] gridExtra_2.3 bookdown_0.41 ## [93] xfun_0.48 rbiom_1.0.3 ## [95] stringi_1.8.4 UCSC.utils_1.1.0 ## [97] lazyeval_0.2.2 yaml_2.3.10 @@ -213,7 +213,7 @@

Session info## [109] jquerylib_0.1.4 Rcpp_1.0.13 ## [111] parallel_4.4.1 pkgdown_2.1.1 ## [113] ggplot2_3.5.1 sparseMatrixStats_1.17.2 -## [115] lme4_1.1-35.5 slam_0.1-53 +## [115] lme4_1.1-35.5 slam_0.1-54 ## [117] mvtnorm_1.3-1 decontam_1.25.0 ## [119] viridisLite_0.4.2 tidytree_0.4.6 ## [121] scales_1.3.0 purrr_1.0.2 diff --git a/articles/minimalgut.html b/articles/minimalgut.html index e04be5d..d175e3e 100644 --- a/articles/minimalgut.html +++ b/articles/minimalgut.html @@ -86,7 +86,7 @@

Sudarshan

Leo Lahti

-

2024-10-20

+

2024-10-29

Source: vignettes/articles/minimalgut.Rmd @@ -422,33 +422,33 @@

Session info## [8] base ## ## other attached packages: -## [1] plyr_1.8.9 miaViz_1.13.10 +## [1] plyr_1.8.9 miaViz_1.13.14 ## [3] ggraph_2.2.1 tidyr_1.3.1 ## [5] tidySummarizedExperiment_1.15.1 ttservice_0.4.1 ## [7] ggplot2_3.5.1 knitr_1.48 ## [9] lubridate_1.9.3 dplyr_1.1.4 -## [11] miaTime_0.1.22 mia_1.13.44 +## [11] miaTime_0.1.22 mia_1.13.47 ## [13] TreeSummarizedExperiment_2.13.0 Biostrings_2.73.2 ## [15] XVector_0.45.0 SingleCellExperiment_1.27.2 -## [17] MultiAssayExperiment_1.31.5 SummarizedExperiment_1.35.2 -## [19] Biobase_2.65.1 GenomicRanges_1.57.1 -## [21] GenomeInfoDb_1.41.1 IRanges_2.39.2 -## [23] S4Vectors_0.43.2 BiocGenerics_0.51.2 -## [25] MatrixGenerics_1.17.0 matrixStats_1.4.1 +## [17] MultiAssayExperiment_1.31.5 SummarizedExperiment_1.35.5 +## [19] Biobase_2.65.1 GenomicRanges_1.57.2 +## [21] GenomeInfoDb_1.41.2 IRanges_2.39.2 +## [23] S4Vectors_0.43.2 BiocGenerics_0.51.3 +## [25] MatrixGenerics_1.17.1 matrixStats_1.4.1 ## [27] BiocStyle_2.33.1 ## ## loaded via a namespace (and not attached): ## [1] splines_4.4.1 ggplotify_0.1.2 ## [3] tibble_3.2.1 polyclip_1.10-7 -## [5] rpart_4.1.23 DirichletMultinomial_1.47.0 +## [5] rpart_4.1.23 DirichletMultinomial_1.47.2 ## [7] lifecycle_1.0.4 lattice_0.22-6 ## [9] MASS_7.3-61 SnowballC_0.7.1 ## [11] backports_1.5.0 magrittr_2.0.3 -## [13] Hmisc_5.1-3 plotly_4.10.4 +## [13] Hmisc_5.2-0 plotly_4.10.4 ## [15] sass_0.4.9 rmarkdown_2.28 ## [17] jquerylib_0.1.4 yaml_2.3.10 ## [19] DBI_1.2.3 minqa_1.2.8 -## [21] abind_1.4-8 zlibbioc_1.51.1 +## [21] abind_1.4-8 zlibbioc_1.51.2 ## [23] purrr_1.0.2 yulab.utils_0.1.7 ## [25] nnet_7.3-19 tweenr_2.0.3 ## [27] sandwich_3.1-1 GenomeInfoDbData_1.2.13 @@ -457,21 +457,21 @@

Session info## [33] vegan_2.6-8 rbiom_1.0.3 ## [35] pkgdown_2.1.1 permute_0.9-7 ## [37] DelayedMatrixStats_1.27.3 codetools_0.2-20 -## [39] DelayedArray_0.31.12 scuttle_1.15.4 +## [39] DelayedArray_0.31.14 scuttle_1.15.5 ## [41] ggforce_0.4.2 tidyselect_1.2.1 ## [43] aplot_0.2.3 UCSC.utils_1.1.0 ## [45] farver_2.1.2 lme4_1.1-35.5 ## [47] ScaledMatrix_1.13.0 viridis_0.6.5 ## [49] base64enc_0.1-3 jsonlite_1.8.9 -## [51] BiocNeighbors_1.99.1 decontam_1.25.0 +## [51] BiocNeighbors_1.99.3 decontam_1.25.0 ## [53] ellipsis_0.3.2 tidygraph_1.3.1 ## [55] Formula_1.2-5 scater_1.33.4 ## [57] systemfonts_1.1.0 ggnewscale_0.5.0 ## [59] tools_4.4.1 treeio_1.29.1 ## [61] ragg_1.3.3 Rcpp_1.0.13 ## [63] glue_1.8.0 gridExtra_2.3 -## [65] SparseArray_1.5.41 xfun_0.48 -## [67] mgcv_1.9-1 withr_3.0.1 +## [65] SparseArray_1.5.45 xfun_0.48 +## [67] mgcv_1.9-1 withr_3.0.2 ## [69] BiocManager_1.30.25 fastmap_1.2.0 ## [71] boot_1.3-31 bluster_1.15.1 ## [73] fansi_1.0.6 digest_0.6.37 @@ -479,22 +479,22 @@

Session info## [77] timechange_0.3.0 R6_2.5.1 ## [79] textshaping_0.4.0 colorspace_2.1-1 ## [81] lpSolve_5.6.21 utf8_1.2.4 -## [83] generics_0.1.3 data.table_1.16.0 -## [85] DECIPHER_3.1.4 graphlayouts_1.2.0 +## [83] generics_0.1.3 data.table_1.16.2 +## [85] DECIPHER_3.1.5 graphlayouts_1.2.0 ## [87] httr_1.4.7 htmlwidgets_1.6.4 -## [89] S4Arrays_1.5.10 pkgconfig_2.0.3 -## [91] gtable_0.3.5 janeaustenr_1.0.0 -## [93] htmltools_0.5.8.1 bookdown_0.40 -## [95] scales_1.3.0 ggfun_0.1.6 -## [97] rstudioapi_0.17.0 reshape2_1.4.4 +## [89] S4Arrays_1.5.11 pkgconfig_2.0.3 +## [91] gtable_0.3.6 janeaustenr_1.0.0 +## [93] htmltools_0.5.8.1 bookdown_0.41 +## [95] scales_1.3.0 ggfun_0.1.7 +## [97] rstudioapi_0.17.1 reshape2_1.4.4 ## [99] checkmate_2.3.2 nlme_3.1-166 ## [101] nloptr_2.1.1 cachem_1.1.0 ## [103] zoo_1.8-12 stringr_1.5.1 ## [105] parallel_4.4.1 vipor_0.4.7 ## [107] foreign_0.8-87 desc_1.4.3 ## [109] pillar_1.9.0 grid_4.4.1 -## [111] vctrs_0.6.5 slam_0.1-53 -## [113] BiocSingular_1.21.4 beachmat_2.21.6 +## [111] vctrs_0.6.5 slam_0.1-54 +## [113] BiocSingular_1.21.4 beachmat_2.21.9 ## [115] cluster_2.1.6 beeswarm_0.4.0 ## [117] htmlTable_2.4.3 evaluate_1.0.1 ## [119] mvtnorm_1.3-1 cli_3.6.3 @@ -504,11 +504,11 @@

Session info## [127] fs_1.6.4 ggbeeswarm_0.7.2 ## [129] stringi_1.8.4 viridisLite_0.4.2 ## [131] BiocParallel_1.39.0 munsell_0.5.1 -## [133] lazyeval_0.2.2 Matrix_1.7-0 +## [133] lazyeval_0.2.2 Matrix_1.7-1 ## [135] patchwork_1.3.0 sparseMatrixStats_1.17.2 -## [137] highr_0.11 igraph_2.0.3 +## [137] highr_0.11 igraph_2.1.1 ## [139] memoise_2.0.1 RcppParallel_5.1.9 -## [141] bslib_0.8.0 ggtree_3.13.1 +## [141] bslib_0.8.0 ggtree_3.13.2 ## [143] ape_5.8 diff --git a/pkgdown.yml b/pkgdown.yml index d29c2a1..f491ad3 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -5,4 +5,4 @@ articles: articles/manipulation: manipulation.html miaTime: miaTime.html articles/minimalgut: minimalgut.html -last_built: 2024-10-20T14:43Z +last_built: 2024-10-29T15:05Z diff --git a/reference/addBaselineDivergence.html b/reference/addBaselineDivergence.html index 4426036..84d2447 100644 --- a/reference/addBaselineDivergence.html +++ b/reference/addBaselineDivergence.html @@ -1,9 +1,7 @@ Beta diversity between the baseline and later time steps — addBaselineDivergence • miaTime @@ -68,9 +66,7 @@

Beta diversity between the baseline and later time steps

Calculates sample dissimilarity between the given baseline and other time points, optionally within a group (subject, reaction chamber, or -similar). The corresponding time difference is returned as well. -The method operates on SummarizedExperiment objects, and the results -are stored in colData.

+similar). The corresponding time difference is returned as well.

@@ -84,8 +80,6 @@

Beta diversity between the baseline and later time steps

reference = NULL, group = NULL, method = "bray", - name = "divergence", - name.time = "time_diff", ... ) @@ -106,13 +100,13 @@

Arguments

...
-

optional arguments passed into +

Optional arguments passed into mia::addDivergence().

time.col
-

Character scalar. Specifies the name of the -time series field in colData.

+

Character scalar. Specifies a name of the column from +colData that identifies the sampling time points for the samples.

assay.type
@@ -121,46 +115,47 @@

Arguments

reference
-

Character vector. Specifies the baseline -sample(s) to be used. If the group argument is given, this must be a -named vector; one element per group.

+

Character scalar. Specifies a name of the column from +colData that identifies the baseline samples to be used. +(Default: NULL)

group
-

Character scalar. Specifies the grouping -factor (name of a colData field). If given, the divergence is calculated -per group. e.g. subject, chamber, group etc. (Default: NULL)

+

Character scalar. Specifies a name of the column from +colData that identifies the grouping of the samples. +(Default: NULL)

method
-

Character scalar. Used to calculate the distance. +

Character scalar. Used to calculate the dissimilarity Method is passed to the function that is specified by dis.fun. (Default: "bray")

name
-

Character scalar. Shows beta diversity between -samples. (Default: "time_divergence")

+

Character scalar. Specifies a column name for storing +divergence results. (Default: "divergence")

name.time
-

Character scalar. Field name for adding the -time difference between samples used to calculate beta diversity. -(Default: "time_difference")

+

Character scalar. Specifies a column name for storing +time differences. (Default: "time_diff")

Value

-

a -SummarizedExperiment +

getBaselineDivergence returns DataFrame object containing the sample dissimilarity and corresponding time difference between -samples (across n time steps), within each level of the grouping factor.

+samples. addBaselineDivergence, on the other hand, returns a +SummarizedExperiment +object with these results in its colData.

Details

-

The group argument allows calculating divergence per group. Otherwise, this -is done across all samples at once.

-

The baseline sample/s always need to belong to the data object i.e. they +

The group argument allows calculating divergence per group. If given, the +divergence is calculated per group. e.g. subject, chamber, group etc. +Otherwise, this is done across all samples at once.

+

The baseline sample(s) always need to belong to the data object i.e. they can be merged into it before applying this function. The reason is that they need to have comparable sample data, at least some time point @@ -170,6 +165,10 @@

Details

the user can provide the baseline vector, or a list of baseline vectors per group (named list per group).

+
+

See also

+

mia::addDivergence()

+

Examples

diff --git a/reference/addStepwiseDivergence.html b/reference/addStepwiseDivergence.html index 6861365..763f0f8 100644 --- a/reference/addStepwiseDivergence.html +++ b/reference/addStepwiseDivergence.html @@ -1,8 +1,6 @@ -Beta diversity between consecutive time steps — addStepwiseDivergence • miaTimeBeta diversity between consecutive time steps — addStepwiseDivergence • miaTime @@ -65,10 +63,8 @@

Beta diversity between consecutive time steps

-

Calculates sample dissimilarity between consecutive time points (t, t+i), -within a group (subject, reaction chamber, or similar). The corresponding -time difference is returned as well. The method operates on -SummarizedExperiment objects, and the results are stored in colData.

+

Calculates sample dissimilarity between consecutive time points along with +time difference.

@@ -82,8 +78,6 @@

Beta diversity between consecutive time steps

time.interval = 1L, group = NULL, method = "bray", - name = "divergence", - name.time = "time_diff", ... ) @@ -104,13 +98,13 @@

Arguments

...
-

optional arguments passed into +

Optional arguments passed into mia::addDivergence().

time.col
-

Character scalar. Specifies the name of the -time series field in colData.

+

Character scalar. Specifies a name of the column from +colData that identifies the sampling time points for the samples.

assay.type
@@ -120,39 +114,53 @@

Arguments

time.interval

Integer scalar. Indicates the increment between -time steps. If you need to take every second, every third, or so, time step -only, then increase this accordingly. (Default: 1L)

+time steps. By default, the function compares each sample to the +previous one. If you need to take every second, every third, or so, time +step, then increase this accordingly. (Default: 1L)

group
-

Character scalar. Specifies the grouping -factor (name of a colData field). If given, the divergence is calculated -per group. e.g. subject, chamber, group etc. (Default: NULL)

+

Character scalar. Specifies a name of the column from +colData that identifies the grouping of the samples. +(Default: NULL)

method
-

Character scalar. Used to calculate the distance. +

Character scalar. Used to calculate the dissimilarity Method is passed to the function that is specified by dis.fun. (Default: "bray")

name
-

Character scalar. Shows beta diversity between -samples. (Default: "time_divergence")

+

Character scalar. Specifies a column name for storing +divergence results. (Default: "divergence")

name.time
-

Character scalar. Field name for adding the -time difference between samples used to calculate beta diversity. -(Default: "time_difference")

+

Character scalar. Specifies a column name for storing +time differences. (Default: "time_diff")

Value

-

a -SummarizedExperiment +

getStepwiseDivergence returns DataFrame object containing the sample dissimilarity and corresponding time difference between -samples (across n time steps), within each level of the grouping factor.

+samples. addStepwiseDivergence, on the other hand, returns a +SummarizedExperiment +object with these results in its colData.

+
+
+

Details

+

These functions calculate time-wise divergence, meaning each sample is +compared to the previous i-th sample, where i is the specified time +interval (see time.interval). By default, the function calculates +divergence by comparing all samples with each other. However, it is often +more meaningful to calculate divergence within a specific patient or group +(see the group parameter).

+
+
+

See also

+

mia::addDivergence()

@@ -164,10 +172,11 @@

Examples

# Calculate divergence tse <- addStepwiseDivergence( - tse, group = "subject", - time_interval = 1, + tse, + group = "subject", + time.interval = 1, time.col = "time", - assay.type="relabundance" + assay.type = "relabundance" )