diff --git a/404.html b/404.html index 7ee7904..291f56c 100644 --- a/404.html +++ b/404.html @@ -38,7 +38,7 @@ lefser - 1.12.1 + 1.12.2 diff --git a/articles/index.html b/articles/index.html index 33f4c67..a52f68c 100644 --- a/articles/index.html +++ b/articles/index.html @@ -23,7 +23,7 @@ lefser - 1.12.1 + 1.12.2 diff --git a/articles/lefser.html b/articles/lefser.html index 4d273be..dd6d553 100644 --- a/articles/lefser.html +++ b/articles/lefser.html @@ -39,7 +39,7 @@ lefser - 1.12.1 + 1.12.2 @@ -82,7 +82,7 @@

Asya Khleborodova, Ludw York

-

2023-11-22

+

2024-03-06

Source: vignettes/lefser.Rmd @@ -174,12 +174,12 @@

Overview and example use of le ## 5 k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Ruminococcaceae|g__Ruminococcus|s__Ruminococcus_sp_5_1_39BFAA|t__GCF_000159975 ## 6 k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium_hallii ## scores -## 1 -6.214370 -## 2 -5.914134 -## 3 -5.902040 -## 4 -5.558476 -## 5 -5.558476 -## 6 -5.480268 +## 1 -6.193941 +## 2 -5.914844 +## 3 -5.903174 +## 4 -5.558376 +## 5 -5.558376 +## 6 -5.507090

Visualizing results with lefserPlot @@ -273,47 +273,47 @@

sessionInfo## [8] base ## ## other attached packages: -## [1] phyloseq_1.46.0 lefser_1.12.1 +## [1] phyloseq_1.46.0 lefser_1.12.2 ## [3] SummarizedExperiment_1.32.0 Biobase_2.62.0 -## [5] GenomicRanges_1.54.1 GenomeInfoDb_1.38.1 -## [7] IRanges_2.36.0 S4Vectors_0.40.1 +## [5] GenomicRanges_1.54.1 GenomeInfoDb_1.38.6 +## [7] IRanges_2.36.0 S4Vectors_0.40.2 ## [9] BiocGenerics_0.48.1 MatrixGenerics_1.14.0 -## [11] matrixStats_1.1.0 BiocStyle_2.30.0 +## [11] matrixStats_1.2.0 BiocStyle_2.30.0 ## ## loaded via a namespace (and not attached): -## [1] bitops_1.0-7 permute_0.9-7 sandwich_3.0-2 -## [4] rlang_1.1.2 magrittr_2.0.3 multcomp_1.4-25 -## [7] ade4_1.7-22 compiler_4.3.2 mgcv_1.9-0 -## [10] systemfonts_1.0.5 vctrs_0.6.4 reshape2_1.4.4 +## [1] bitops_1.0-7 permute_0.9-7 sandwich_3.1-0 +## [4] rlang_1.1.3 magrittr_2.0.3 multcomp_1.4-25 +## [7] ade4_1.7-22 compiler_4.3.2 mgcv_1.9-1 +## [10] systemfonts_1.0.5 vctrs_0.6.5 reshape2_1.4.4 ## [13] stringr_1.5.1 pkgconfig_2.0.3 crayon_1.5.2 ## [16] fastmap_1.1.1 XVector_0.42.0 labeling_0.4.3 -## [19] utf8_1.2.4 rmarkdown_2.25 ragg_1.2.6 -## [22] purrr_1.0.2 xfun_0.41 modeltools_0.2-23 -## [25] zlibbioc_1.48.0 cachem_1.0.8 jsonlite_1.8.7 +## [19] utf8_1.2.4 rmarkdown_2.25 ragg_1.2.7 +## [22] purrr_1.0.2 xfun_0.42 modeltools_0.2-23 +## [25] zlibbioc_1.48.0 cachem_1.0.8 jsonlite_1.8.8 ## [28] biomformat_1.30.0 highr_0.10 rhdf5filters_1.14.1 -## [31] DelayedArray_0.28.0 Rhdf5lib_1.24.0 parallel_4.3.2 -## [34] cluster_2.1.4 R6_2.5.1 coin_1.4-3 -## [37] bslib_0.5.1 stringi_1.8.1 jquerylib_0.1.4 -## [40] Rcpp_1.0.11 bookdown_0.36 iterators_1.0.14 -## [43] knitr_1.45 zoo_1.8-12 Matrix_1.6-3 -## [46] splines_4.3.2 igraph_1.5.1 tidyselect_1.2.0 -## [49] abind_1.4-5 yaml_2.3.7 vegan_2.6-4 +## [31] DelayedArray_0.28.0 Rhdf5lib_1.24.2 parallel_4.3.2 +## [34] cluster_2.1.6 R6_2.5.1 coin_1.4-3 +## [37] bslib_0.6.1 stringi_1.8.3 jquerylib_0.1.4 +## [40] Rcpp_1.0.12 bookdown_0.38 iterators_1.0.14 +## [43] knitr_1.45 zoo_1.8-12 Matrix_1.6-5 +## [46] splines_4.3.2 igraph_2.0.2 tidyselect_1.2.0 +## [49] abind_1.4-5 yaml_2.3.8 vegan_2.6-4 ## [52] codetools_0.2-19 lattice_0.22-5 tibble_3.2.1 -## [55] plyr_1.8.9 withr_2.5.2 evaluate_0.23 -## [58] desc_1.4.2 survival_3.5-7 Biostrings_2.70.1 +## [55] plyr_1.8.9 withr_3.0.0 evaluate_0.23 +## [58] desc_1.4.3 survival_3.5-8 Biostrings_2.70.2 ## [61] pillar_1.9.0 BiocManager_1.30.22 foreach_1.5.2 -## [64] generics_0.1.3 rprojroot_2.0.4 RCurl_1.98-1.13 -## [67] ggplot2_3.4.4 munsell_0.5.0 scales_1.2.1 -## [70] glue_1.6.2 tools_4.3.2 data.table_1.14.8 -## [73] fs_1.6.3 mvtnorm_1.2-3 rhdf5_2.46.0 -## [76] grid_4.3.2 ape_5.7-1 libcoin_1.0-10 -## [79] colorspace_2.1-0 nlme_3.1-163 GenomeInfoDbData_1.2.11 -## [82] cli_3.6.1 textshaping_0.3.7 fansi_1.0.5 -## [85] S4Arrays_1.2.0 dplyr_1.1.4 gtable_0.3.4 -## [88] sass_0.4.7 digest_0.6.33 SparseArray_1.2.2 -## [91] TH.data_1.1-2 farver_2.1.1 memoise_2.0.1 -## [94] htmltools_0.5.7 pkgdown_2.0.7 multtest_2.58.0 -## [97] lifecycle_1.0.4 MASS_7.3-60 +## [64] generics_0.1.3 RCurl_1.98-1.14 ggplot2_3.5.0 +## [67] munsell_0.5.0 scales_1.3.0 glue_1.7.0 +## [70] tools_4.3.2 data.table_1.15.2 fs_1.6.3 +## [73] mvtnorm_1.2-4 rhdf5_2.46.1 grid_4.3.2 +## [76] ape_5.7-1 libcoin_1.0-10 colorspace_2.1-0 +## [79] nlme_3.1-164 GenomeInfoDbData_1.2.11 cli_3.6.2 +## [82] textshaping_0.3.7 fansi_1.0.6 S4Arrays_1.2.1 +## [85] dplyr_1.1.4 gtable_0.3.4 sass_0.4.8 +## [88] digest_0.6.34 SparseArray_1.2.4 TH.data_1.1-2 +## [91] farver_2.1.1 memoise_2.0.1 htmltools_0.5.7 +## [94] pkgdown_2.0.7 multtest_2.58.0 lifecycle_1.0.4 +## [97] MASS_7.3-60.0.1

diff --git a/articles/lefser_files/figure-html/unnamed-chunk-8-1.png b/articles/lefser_files/figure-html/unnamed-chunk-8-1.png index 51ee636..4e2fe1f 100644 Binary files a/articles/lefser_files/figure-html/unnamed-chunk-8-1.png and b/articles/lefser_files/figure-html/unnamed-chunk-8-1.png differ diff --git a/authors.html b/authors.html index 5817e2a..49de6af 100644 --- a/authors.html +++ b/authors.html @@ -23,7 +23,7 @@ lefser - 1.12.1 + 1.12.2 @@ -86,15 +86,15 @@

Citation

-

Khleborodova A (2023). +

Khleborodova A (2024). lefser: R implementation of the LEfSE method for microbiome biomarker discovery. -R package version 1.12.1, https://github.com/waldronlab/lefser. +R package version 1.12.2, https://github.com/waldronlab/lefser. 

@Manual{,
   title = {lefser: R implementation of the LEfSE method for microbiome biomarker discovery},
   author = {Asya Khleborodova},
-  year = {2023},
-  note = {R package version 1.12.1},
+  year = {2024},
+  note = {R package version 1.12.2},
   url = {https://github.com/waldronlab/lefser},
 }
diff --git a/index.html b/index.html index 32ecbf6..702dda8 100644 --- a/index.html +++ b/index.html @@ -42,7 +42,7 @@ lefser - 1.12.1 + 1.12.2 diff --git a/news/index.html b/news/index.html index cd79e79..bbf536b 100644 --- a/news/index.html +++ b/news/index.html @@ -23,7 +23,7 @@ lefser - 1.12.1 + 1.12.2 diff --git a/pkgdown.yml b/pkgdown.yml index 093096b..100fd57 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -3,7 +3,7 @@ pkgdown: 2.0.7 pkgdown_sha: ~ articles: lefser: lefser.html -last_built: 2023-11-22T16:50Z +last_built: 2024-03-06T15:46Z urls: reference: https://waldronlab.io/lefser/reference article: https://waldronlab.io/lefser/articles diff --git a/reference/index.html b/reference/index.html index 749931a..f7777a8 100644 --- a/reference/index.html +++ b/reference/index.html @@ -23,7 +23,7 @@ lefser - 1.12.1 + 1.12.2 diff --git a/reference/lefser.html b/reference/lefser.html index 16bcaee..8867989 100644 --- a/reference/lefser.html +++ b/reference/lefser.html @@ -27,7 +27,7 @@ lefser - 1.12.1 + 1.12.2 @@ -178,12 +178,12 @@

Examples

#> 5 k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus_eutactus #> 6 k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus_eutactus|t__GCF_000154425 #> scores -#> 1 -6.336653 -#> 2 -6.336653 -#> 3 -6.336612 -#> 4 -5.757507 -#> 5 -5.506376 -#> 6 -5.492191 +#> 1 -6.364356 +#> 2 -6.364356 +#> 3 -6.364325 +#> 4 -5.791754 +#> 5 -5.622091 +#> 6 -5.566016 # (2) Using classes and sublasses data(zeller14) @@ -197,19 +197,19 @@

Examples

#> See `?factor` or `?relevel` to change the reference category. head(res_block) #> Names -#> 1 k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae -#> 2 k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium +#> 1 k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium +#> 2 k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae #> 3 k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas -#> 4 k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas_asaccharolytica -#> 5 k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas_asaccharolytica|t__Porphyromonas_asaccharolytica_unclassified -#> 6 k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus_stomatis +#> 4 k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas_asaccharolytica|t__Porphyromonas_asaccharolytica_unclassified +#> 5 k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas_asaccharolytica +#> 6 k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales #> scores -#> 1 -5.183721 -#> 2 -5.145483 -#> 3 -4.969229 -#> 4 -4.886948 -#> 5 -4.879742 -#> 6 -4.794062 +#> 1 -5.233182 +#> 2 -5.212977 +#> 3 -5.039454 +#> 4 -4.987723 +#> 5 -4.932632 +#> 6 -4.840816 diff --git a/reference/lefserPlot-1.png b/reference/lefserPlot-1.png index c41a875..de2a879 100644 Binary files a/reference/lefserPlot-1.png and b/reference/lefserPlot-1.png differ diff --git a/reference/lefserPlot.html b/reference/lefserPlot.html index 4a032ac..b79c0c6 100644 --- a/reference/lefserPlot.html +++ b/reference/lefserPlot.html @@ -24,7 +24,7 @@ lefser - 1.12.1 + 1.12.2 @@ -112,15 +112,15 @@

Examples

#> 2 k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales #> 3 k__Bacteria|p__Bacteroidetes #> 4 k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae -#> 5 k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus_eutactus -#> 6 k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus_eutactus|t__GCF_000154425 +#> 5 k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus_eutactus|t__GCF_000154425 +#> 6 k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus_eutactus #> scores -#> 1 -6.328647 -#> 2 -6.328647 -#> 3 -6.328595 -#> 4 -5.749317 -#> 5 -5.550262 -#> 6 -5.538754 +#> 1 -6.406226 +#> 2 -6.406226 +#> 3 -6.406201 +#> 4 -5.758285 +#> 5 -5.638205 +#> 6 -5.593375 #> #> lefser> # (2) Using classes and sublasses #> lefser> data(zeller14) @@ -136,20 +136,20 @@

Examples

#> See `?factor` or `?relevel` to change the reference category. #> #> lefser> head(res_block) -#> Names -#> 1 k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae -#> 2 k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium -#> 3 k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas -#> 4 k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas_asaccharolytica -#> 5 k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas_asaccharolytica|t__Porphyromonas_asaccharolytica_unclassified -#> 6 k__Bacteria|p__Fusobacteria|c__Fusobacteriia +#> Names +#> 1 k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae +#> 2 k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium +#> 3 k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas +#> 4 k__Bacteria|p__Fusobacteria +#> 5 k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales +#> 6 k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas_asaccharolytica #> scores -#> 1 -5.229792 -#> 2 -5.216477 -#> 3 -5.017874 -#> 4 -4.953679 -#> 5 -4.938438 -#> 6 -4.857611 +#> 1 -5.331489 +#> 2 -5.232178 +#> 3 -5.051428 +#> 4 -4.924990 +#> 5 -4.923957 +#> 6 -4.922982 lefserPlot(res_group) diff --git a/reference/relativeAb.html b/reference/relativeAb.html index 3b39ae2..beeaa92 100644 --- a/reference/relativeAb.html +++ b/reference/relativeAb.html @@ -1,6 +1,8 @@ Utility function to calculate relative abundances — relativeAb • lefser