Last updated: 2021-01-14
Checks: 7 0
Knit directory: esoph-micro-cancer-workflow/
This reproducible R Markdown analysis was created with workflowr (version 1.6.2). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.
Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.
Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.
The command set.seed(20200916) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.
Great job! Recording the operating system, R version, and package versions is critical for reproducibility.
Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.
Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.
Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.
The results in this page were generated with repository version e6b4c7f. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.
Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:
Ignored files:
Ignored: .Rhistory
Ignored: .Rproj.user/
Ignored: data/
Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.
These are the previous versions of the repository in which changes were made to the R Markdown (analysis/results-question-2.Rmd) and HTML (docs/results-question-2.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.
| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | e6b4c7f | noah-padgett | 2021-01-14 | meeting update |
| html | e6b4c7f | noah-padgett | 2021-01-14 | meeting update |
Q1: is there a taxonomic signature shared between the barrett's samples?# in long format
table(dat.16s$sample_type)
0 Barretts Only
19800 1320
EAC-adjacent tissue w/ Barretts History EAC tissues w/ Barretts History
11352 9240 dat <- dat.16s %>% filter(OTU == "Fusobacterium_nucleatum")
table(dat$sample_type)
0 Barretts Only
75 5
EAC-adjacent tissue w/ Barretts History EAC tissues w/ Barretts History
43 35 table(dat$Barretts.)
N Y
71 87 dat.16s.s %>%
filter(sample_type != "0") %>%
dplyr::group_by(sample_type, Genus)%>%
dplyr::summarise(
m = mean(Abundance, na.rm=T)
) %>%
kable(format="html") %>%
kable_styling(full_width = T) %>%
scroll_box()`summarise()` regrouping output by 'sample_type' (override with `.groups` argument)| sample_type | Genus | m |
|---|---|---|
| Barretts Only | g__Campylobacter | 0.0036000 |
| Barretts Only | g__Fusobacterium | 0.0060000 |
| Barretts Only | g__Prevotella | 0.0652000 |
| Barretts Only | g__Streptococcus | 0.4572000 |
| EAC-adjacent tissue w/ Barretts History | g__Campylobacter | 0.0027442 |
| EAC-adjacent tissue w/ Barretts History | g__Fusobacterium | 0.0197694 |
| EAC-adjacent tissue w/ Barretts History | g__Prevotella | 0.0641215 |
| EAC-adjacent tissue w/ Barretts History | g__Streptococcus | 0.2147100 |
| EAC tissues w/ Barretts History | g__Campylobacter | 0.0097714 |
| EAC tissues w/ Barretts History | g__Fusobacterium | 0.0491790 |
| EAC tissues w/ Barretts History | g__Prevotella | 0.0485287 |
| EAC tissues w/ Barretts History | g__Streptococcus | 0.2641698 |
dat.16s.s %>%
filter(sample_type != "0") %>%
dplyr::group_by(sample_type, Phylum)%>%
dplyr::summarise(
m = mean(Abundance, na.rm=T)
) %>%
kable(format="html") %>%
kable_styling(full_width = T) %>%
scroll_box()`summarise()` regrouping output by 'sample_type' (override with `.groups` argument)| sample_type | Phylum | m |
|---|---|---|
| Barretts Only | p__Bacteroidetes | 0.0652000 |
| Barretts Only | p__Firmicutes | 0.4572000 |
| Barretts Only | p__Fusobacteria | 0.0060000 |
| Barretts Only | p__Proteobacteria | 0.0036000 |
| EAC-adjacent tissue w/ Barretts History | p__Bacteroidetes | 0.0641215 |
| EAC-adjacent tissue w/ Barretts History | p__Firmicutes | 0.2147100 |
| EAC-adjacent tissue w/ Barretts History | p__Fusobacteria | 0.0197694 |
| EAC-adjacent tissue w/ Barretts History | p__Proteobacteria | 0.0027442 |
| EAC tissues w/ Barretts History | p__Bacteroidetes | 0.0485287 |
| EAC tissues w/ Barretts History | p__Firmicutes | 0.2641698 |
| EAC tissues w/ Barretts History | p__Fusobacteria | 0.0491790 |
| EAC tissues w/ Barretts History | p__Proteobacteria | 0.0097714 |
# in long format
table(dat.rna$sample_type)
0 EAC-adjacent tissue w/ Barretts History
112176 2337
EAC tissues w/ Barretts History
20254 dat <- dat.rna %>% filter(otu2 == "Fusobacterium nucleatum")
table(dat$sample_type)
0 EAC-adjacent tissue w/ Barretts History
144 3
EAC tissues w/ Barretts History
26 table(dat$Barrett.s.Esophagus.Reported)
No Not Available Yes
113 31 29 dat.rna.s %>%
filter(sample_type != "0") %>%
dplyr::group_by(sample_type, Genus)%>%
dplyr::summarise(
m = mean(Abundance, na.rm=T)
) %>%
kable(format="html") %>%
kable_styling(full_width = T) %>%
scroll_box()`summarise()` regrouping output by 'sample_type' (override with `.groups` argument)| sample_type | Genus | m |
|---|---|---|
| EAC-adjacent tissue w/ Barretts History | Campylobacter | 0.0000000 |
| EAC-adjacent tissue w/ Barretts History | Fusobacterium | 0.0000797 |
| EAC-adjacent tissue w/ Barretts History | Prevotella | 0.0001644 |
| EAC-adjacent tissue w/ Barretts History | Streptococcus | 0.0000554 |
| EAC tissues w/ Barretts History | Campylobacter | 0.0000218 |
| EAC tissues w/ Barretts History | Fusobacterium | 0.0004995 |
| EAC tissues w/ Barretts History | Prevotella | 0.0000900 |
| EAC tissues w/ Barretts History | Streptococcus | 0.0001505 |
dat.rna.s %>%
filter(sample_type != "0") %>%
dplyr::group_by(sample_type, Phylum)%>%
dplyr::summarise(
m = mean(Abundance, na.rm=T)
) %>%
kable(format="html") %>%
kable_styling(full_width = T) %>%
scroll_box()`summarise()` regrouping output by 'sample_type' (override with `.groups` argument)| sample_type | Phylum | m |
|---|---|---|
| EAC-adjacent tissue w/ Barretts History | Bacteroidetes | 0.0001644 |
| EAC-adjacent tissue w/ Barretts History | Firmicutes | 0.0000554 |
| EAC-adjacent tissue w/ Barretts History | Fusobacteria | 0.0000797 |
| EAC-adjacent tissue w/ Barretts History | Proteobacteria | 0.0000000 |
| EAC tissues w/ Barretts History | Bacteroidetes | 0.0000900 |
| EAC tissues w/ Barretts History | Firmicutes | 0.0001505 |
| EAC tissues w/ Barretts History | Fusobacteria | 0.0004995 |
| EAC tissues w/ Barretts History | Proteobacteria | 0.0000218 |
# in long format
table(dat.wgs$sample_type)
0 EAC-adjacent tissue w/ Barretts History
100491 4674
EAC tissues w/ Barretts History
3116 dat <- dat.wgs %>% filter(otu2 == "Fusobacterium nucleatum")
table(dat$sample_type)
0 EAC-adjacent tissue w/ Barretts History
129 6
EAC tissues w/ Barretts History
4 table(dat$Barrett.s.Esophagus.Reported)
No Not Available Yes
54 47 10 dat.wgs.s %>%
filter(sample_type != "0") %>%
dplyr::group_by(sample_type, Genus)%>%
dplyr::summarise(
m = mean(Abundance, na.rm=T)
) %>%
kable(format="html") %>%
kable_styling(full_width = T) %>%
scroll_box()`summarise()` regrouping output by 'sample_type' (override with `.groups` argument)| sample_type | Genus | m |
|---|---|---|
| EAC-adjacent tissue w/ Barretts History | Campylobacter | 0.0000441 |
| EAC-adjacent tissue w/ Barretts History | Fusobacterium | 0.0012641 |
| EAC-adjacent tissue w/ Barretts History | Prevotella | 0.0014830 |
| EAC-adjacent tissue w/ Barretts History | Streptococcus | 0.0031405 |
| EAC tissues w/ Barretts History | Campylobacter | 0.0000303 |
| EAC tissues w/ Barretts History | Fusobacterium | 0.0005612 |
| EAC tissues w/ Barretts History | Prevotella | 0.0009216 |
| EAC tissues w/ Barretts History | Streptococcus | 0.0006834 |
dat.wgs.s %>%
filter(sample_type != "0") %>%
dplyr::group_by(sample_type, Phylum)%>%
dplyr::summarise(
m = mean(Abundance, na.rm=T)
) %>%
kable(format="html") %>%
kable_styling(full_width = T) %>%
scroll_box()`summarise()` regrouping output by 'sample_type' (override with `.groups` argument)| sample_type | Phylum | m |
|---|---|---|
| EAC-adjacent tissue w/ Barretts History | Bacteroidetes | 0.0014830 |
| EAC-adjacent tissue w/ Barretts History | Firmicutes | 0.0031405 |
| EAC-adjacent tissue w/ Barretts History | Fusobacteria | 0.0012641 |
| EAC-adjacent tissue w/ Barretts History | Proteobacteria | 0.0000441 |
| EAC tissues w/ Barretts History | Bacteroidetes | 0.0009216 |
| EAC tissues w/ Barretts History | Firmicutes | 0.0006834 |
| EAC tissues w/ Barretts History | Fusobacteria | 0.0005612 |
| EAC tissues w/ Barretts History | Proteobacteria | 0.0000303 |
sessionInfo()R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] car_3.0-8 carData_3.0-4 gvlma_1.0.0.3 patchwork_1.0.1
[5] viridis_0.5.1 viridisLite_0.3.0 gridExtra_2.3 xtable_1.8-4
[9] kableExtra_1.1.0 plyr_1.8.6 data.table_1.13.0 readxl_1.3.1
[13] forcats_0.5.0 stringr_1.4.0 dplyr_1.0.1 purrr_0.3.4
[17] readr_1.3.1 tidyr_1.1.1 tibble_3.0.3 ggplot2_3.3.2
[21] tidyverse_1.3.0 lmerTest_3.1-2 lme4_1.1-23 Matrix_1.2-18
[25] vegan_2.5-6 lattice_0.20-41 permute_0.9-5 phyloseq_1.32.0
[29] workflowr_1.6.2
loaded via a namespace (and not attached):
[1] minqa_1.2.4 colorspace_1.4-1 rio_0.5.16
[4] ellipsis_0.3.1 rprojroot_1.3-2 XVector_0.28.0
[7] fs_1.5.0 rstudioapi_0.11 fansi_0.4.1
[10] lubridate_1.7.9 xml2_1.3.2 codetools_0.2-16
[13] splines_4.0.2 knitr_1.29 ade4_1.7-15
[16] jsonlite_1.7.0 nloptr_1.2.2.2 broom_0.7.0
[19] cluster_2.1.0 dbplyr_1.4.4 BiocManager_1.30.10
[22] compiler_4.0.2 httr_1.4.2 backports_1.1.7
[25] assertthat_0.2.1 cli_2.0.2 later_1.1.0.1
[28] htmltools_0.5.0 tools_4.0.2 igraph_1.2.5
[31] gtable_0.3.0 glue_1.4.1 reshape2_1.4.4
[34] Rcpp_1.0.5 Biobase_2.48.0 cellranger_1.1.0
[37] vctrs_0.3.2 Biostrings_2.56.0 multtest_2.44.0
[40] ape_5.4 nlme_3.1-148 iterators_1.0.12
[43] xfun_0.19 openxlsx_4.1.5 rvest_0.3.6
[46] lifecycle_0.2.0 statmod_1.4.34 zlibbioc_1.34.0
[49] MASS_7.3-51.6 scales_1.1.1 hms_0.5.3
[52] promises_1.1.1 parallel_4.0.2 biomformat_1.16.0
[55] rhdf5_2.32.2 curl_4.3 yaml_2.2.1
[58] stringi_1.4.6 highr_0.8 S4Vectors_0.26.1
[61] foreach_1.5.0 BiocGenerics_0.34.0 zip_2.0.4
[64] boot_1.3-25 rlang_0.4.7 pkgconfig_2.0.3
[67] evaluate_0.14 Rhdf5lib_1.10.1 tidyselect_1.1.0
[70] magrittr_1.5 R6_2.4.1 IRanges_2.22.2
[73] generics_0.0.2 DBI_1.1.0 foreign_0.8-80
[76] pillar_1.4.6 haven_2.3.1 whisker_0.4
[79] withr_2.2.0 mgcv_1.8-31 abind_1.4-5
[82] survival_3.2-3 modelr_0.1.8 crayon_1.3.4
[85] rmarkdown_2.5 grid_4.0.2 blob_1.2.1
[88] git2r_0.27.1 reprex_0.3.0 digest_0.6.25
[91] webshot_0.5.2 httpuv_1.5.4 numDeriv_2016.8-1.1
[94] stats4_4.0.2 munsell_0.5.0