Chapter 3 Quality Control
Loading packages
The taxonomic levels of spike-in sample’s bacteria is species. Firstly, using the summarize_taxa to get the species level phyloseq object and then do run_RefCheck under the optimal parameters.
3.1 spike-in sample (BRS)
- get the BRS_ID
metaphlan2_ps_LOD_species <- aggregate_LOD_taxa(ps = metaphlan2_ps,
taxa_level = "Species",
cutoff = 1e-04)
metaphlan2_ps_LOD_species@sam_data## Group phynotype
## s1 BB 0.00
## s2 AA 2.50
## s3 BB 0.00
## s4 AA 1.25
## s5 AA 30.00
## s6 AA 15.00
## s7 BB 8.75
## s8 BB 0.00
## s9 BB 3.75
## s10 BB 2.50
## s11 BB 15.00
## s12 BB 2.50
## s13 BB 2.50
## s14 BB 0.00
## s15 BB 1.07
## s16 BB 2.50
## s17 AA 5.00
## s18 BB 35.00
## s19 BB 7.50
## s20 BB 15.00
## s21 AA 3.75
## s22 AA 3.75
## refE QC NA- run
run_RefCheck2
## Noting: the Reference Matrix is for MGS
##
## ############Matched baterica of the BRS sample#############
## The number of BRS' bacteria matched the Reference Matrix is [15]
## s__Bifidobacterium_adolescentis
## s__Bifidobacterium_longum
## s__Bifidobacterium_pseudocatenulatum
## s__Collinsella_aerofaciens
## s__Bacteroides_ovatus
## s__Bacteroides_thetaiotaomicron
## s__Bacteroides_uniformis
## s__Bacteroides_vulgatus
## s__Bacteroides_xylanisolvens
## s__Prevotella_copri
## s__Streptococcus_salivarius
## s__Coprococcus_comes
## s__Dorea_formicigenerans
## s__Roseburia_hominis
## s__Faecalibacterium_prausnitzii
## The number of bacteria unmatched the Reference Matrix is [11]
## s__Propionibacterium_acnes
## s__Bifidobacterium_bifidum
## s__Eggerthella_unclassified
## s__Bacteroides_fragilis
## s__Bacteroides_intestinalis
## s__Parabacteroides_goldsteinii
## s__Enterococcus_faecalis
## s__Enterococcus_faecium
## s__Lactobacillus_pentosus
## s__Lactobacillus_salivarius
## s__Escherichia_coli
## The number of the additional bacteria compared to the Reference Matrix is [45]
## ###########################################################
##
## ##################Status of the BRS sample##################
## Whether the BRS has the all bateria of Reference Matrix: FALSE
## Correlation Coefficient of the BRS is: -0.1179
## Bray Curtis of the BRS is: 0.8761
## Impurity of the BRS is: 32.76
## ###########################################################
## #####Final Evaluation Results of the BRS #######
## The BRS of sequencing dataset didn't pass the cutoff of the Reference Matrix
## ###########################################################
## $Matrix
## 7682 7683 7684 7685 7842 7843 7844 7845 refE mean
## Propionibacterium_acnes 0.28649 0.22355 0.32199 0.28276 0.37568 0.44201 0.41135 0.39489 NA 0.30430222
## Bifidobacterium_adolescentis 7.05611 6.28460 6.57297 6.25448 4.69357 4.80628 4.94943 4.84278 0.04649 5.05630111
## Bifidobacterium_bifidum 1.32803 1.19346 1.26883 1.05154 1.34640 1.40471 1.43721 1.48097 NA 1.16790556
## Bifidobacterium_longum 10.31832 9.25812 9.69184 7.76031 11.03311 11.61484 12.29030 11.69019 0.01646 9.29705444
## Bifidobacterium_pseudocatenulatum 6.89760 6.36177 7.39605 5.76804 6.19464 6.47094 7.41615 6.27837 0.15023 5.88153222
## Collinsella_aerofaciens 0.56189 0.53249 0.60476 0.47934 0.65513 0.68833 0.76063 0.66896 0.07251 0.55822667
## Eggerthella_unclassified 1.21416 1.06143 1.19122 0.85743 1.36030 1.48457 1.61204 1.50700 NA 1.14312778
## Bacteroides_fragilis 6.56752 7.19828 7.27658 7.31998 7.10174 6.70626 6.60219 6.11088 NA 6.09815889
## Bacteroides_intestinalis 0.09448 0.09550 0.10216 0.09326 0.08448 0.09556 0.08852 0.10469 NA 0.08429444
## Bacteroides_ovatus 3.08552 3.27226 3.10904 3.24565 3.51376 3.50063 3.37872 3.42300 0.25782 2.97626667
## Bacteroides_thetaiotaomicron 3.24207 3.31897 3.22418 3.43809 3.35611 3.38323 3.29098 3.30355 1.47422 3.11460000
## Bacteroides_uniformis 2.24271 2.24035 1.92015 2.18435 2.43230 2.38180 2.13830 2.41437 0.21061 2.01832667
## Bacteroides_vulgatus 3.06672 3.20369 3.14979 3.15352 3.24822 3.09280 3.13038 3.06113 2.14684 3.02812111
## Bacteroides_xylanisolvens 1.55687 1.84824 1.91166 1.85273 1.75220 1.74002 1.69811 1.67676 0.32466 1.59569444
## Parabacteroides_goldsteinii 5.92564 5.95499 6.04638 5.85282 6.85811 6.50800 6.35758 6.96646 NA 5.60777556
## Prevotella_copri 2.03757 1.99619 1.92504 2.15422 1.57638 1.60584 1.57913 1.59224 60.84109 8.36752222
## Enterococcus_faecalis 11.46695 12.46200 11.92117 11.95884 13.71474 13.67805 13.21782 13.27297 NA 11.29917111
## Enterococcus_faecium 4.57147 4.64943 4.52463 4.76407 5.45590 5.17641 5.15276 5.24896 NA 4.39373667
## Lactobacillus_pentosus 0.75844 0.75524 0.72958 0.80796 0.91548 0.89940 0.81308 0.94831 NA 0.73638778
## Lactobacillus_salivarius 4.89005 5.18462 5.12745 7.79194 2.72469 2.25673 2.10356 2.02202 NA 3.56678444
## Streptococcus_salivarius 3.54220 3.74119 3.62036 4.01546 2.90216 2.70193 2.61760 2.57348 0.02846 2.86031556
## Coprococcus_comes 2.28009 2.42978 2.25227 2.82904 1.21527 1.16485 1.07160 1.07834 0.01444 1.59285333
## Dorea_formicigenerans 4.83413 5.02149 5.18268 5.56891 3.34720 3.09877 3.08677 2.70732 0.02775 3.65278000
## Roseburia_hominis 0.04384 0.04183 0.04107 0.02304 0.03853 0.03464 0.03532 0.03597 0.01307 0.03414556
## Faecalibacterium_prausnitzii 0.65572 0.60153 0.60112 0.62079 0.54147 0.55383 0.58806 0.54655 1.61939 0.70316222
## Escherichia_coli 8.76957 8.33337 7.70416 8.11247 10.44118 10.33823 9.96261 11.06988 NA 8.30349667
## Impurity_level 2.70584 2.73563 2.58287 1.75896 3.12125 4.17134 4.20980 4.97996 32.76000 6.55840556
## Evaluation
## Propionibacterium_acnes refE didn't pass the threshold (2023-10-27 16:59:12).
## Bifidobacterium_adolescentis refE didn't pass the threshold (2023-10-27 16:59:12).
## Bifidobacterium_bifidum refE didn't pass the threshold (2023-10-27 16:59:12).
## Bifidobacterium_longum refE didn't pass the threshold (2023-10-27 16:59:12).
## Bifidobacterium_pseudocatenulatum refE didn't pass the threshold (2023-10-27 16:59:12).
## Collinsella_aerofaciens refE didn't pass the threshold (2023-10-27 16:59:12).
## Eggerthella_unclassified refE didn't pass the threshold (2023-10-27 16:59:12).
## Bacteroides_fragilis refE didn't pass the threshold (2023-10-27 16:59:12).
## Bacteroides_intestinalis refE didn't pass the threshold (2023-10-27 16:59:12).
## Bacteroides_ovatus refE didn't pass the threshold (2023-10-27 16:59:12).
## Bacteroides_thetaiotaomicron refE didn't pass the threshold (2023-10-27 16:59:12).
## Bacteroides_uniformis refE didn't pass the threshold (2023-10-27 16:59:12).
## Bacteroides_vulgatus refE didn't pass the threshold (2023-10-27 16:59:12).
## Bacteroides_xylanisolvens refE didn't pass the threshold (2023-10-27 16:59:12).
## Parabacteroides_goldsteinii refE didn't pass the threshold (2023-10-27 16:59:12).
## Prevotella_copri refE didn't pass the threshold (2023-10-27 16:59:12).
## Enterococcus_faecalis refE didn't pass the threshold (2023-10-27 16:59:12).
## Enterococcus_faecium refE didn't pass the threshold (2023-10-27 16:59:12).
## Lactobacillus_pentosus refE didn't pass the threshold (2023-10-27 16:59:12).
## Lactobacillus_salivarius refE didn't pass the threshold (2023-10-27 16:59:12).
## Streptococcus_salivarius refE didn't pass the threshold (2023-10-27 16:59:12).
## Coprococcus_comes refE didn't pass the threshold (2023-10-27 16:59:12).
## Dorea_formicigenerans refE didn't pass the threshold (2023-10-27 16:59:12).
## Roseburia_hominis refE didn't pass the threshold (2023-10-27 16:59:12).
## Faecalibacterium_prausnitzii refE didn't pass the threshold (2023-10-27 16:59:12).
## Escherichia_coli refE didn't pass the threshold (2023-10-27 16:59:12).
## Impurity_level refE didn't pass the threshold (2023-10-27 16:59:12).
##
## $Assess
## Gold_Cutoff BRS
## Coef 0.8726 -0.1179
## Bray 0.2064 0.8761
## Impurity 6.4400 32.76003.2 Spike-in sample’s (BRS) remove
metaphlan2_ps_LOD_species_remove_BRS <- get_GroupPhyloseq(
ps = metaphlan2_ps_LOD_species,
group = "Group",
group_names = "QC",
discard = TRUE)
metaphlan2_ps_LOD_species_remove_BRS## phyloseq-class experiment-level object
## otu_table() OTU Table: [ 192 taxa and 22 samples ]
## sample_data() Sample Data: [ 22 samples by 2 sample variables ]
## tax_table() Taxonomy Table: [ 192 taxa by 7 taxonomic ranks ]3.3 Systematic Information
## ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
## setting value
## version R version 4.1.3 (2022-03-10)
## os macOS Monterey 12.2.1
## system x86_64, darwin17.0
## ui RStudio
## language (EN)
## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz Asia/Shanghai
## date 2023-10-27
## rstudio 2023.09.0+463 Desert Sunflower (desktop)
## pandoc 3.1.1 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/ (via rmarkdown)
##
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## openssl 2.0.6 2023-03-09 [2] CRAN (R 4.1.2)
## pbapply 1.7-2 2023-06-27 [2] CRAN (R 4.1.3)
## pbivnorm 0.6.0 2015-01-23 [2] CRAN (R 4.1.0)
## pcaPP 2.0-3 2022-10-24 [2] CRAN (R 4.1.2)
## permute * 0.9-7 2022-01-27 [2] CRAN (R 4.1.2)
## pheatmap * 1.0.12 2019-01-04 [2] CRAN (R 4.1.0)
## phyloseq * 1.38.0 2021-10-26 [2] Bioconductor
## picante * 1.8.2 2020-06-10 [2] CRAN (R 4.1.0)
## pillar 1.9.0 2023-03-22 [2] CRAN (R 4.1.2)
## pkgbuild 1.4.2 2023-06-26 [2] CRAN (R 4.1.3)
## pkgconfig 2.0.3 2019-09-22 [2] CRAN (R 4.1.0)
## pkgload 1.3.2.1 2023-07-08 [2] CRAN (R 4.1.3)
## plyr 1.8.8 2022-11-11 [2] CRAN (R 4.1.2)
## png 0.1-8 2022-11-29 [2] CRAN (R 4.1.2)
## ppcor 1.1 2015-12-03 [2] CRAN (R 4.1.0)
## preprocessCore 1.56.0 2021-10-26 [2] Bioconductor
## prettyunits 1.1.1 2020-01-24 [2] CRAN (R 4.1.0)
## processx 3.8.2 2023-06-30 [2] CRAN (R 4.1.3)
## profvis 0.3.8 2023-05-02 [2] CRAN (R 4.1.2)
## promises 1.2.0.1 2021-02-11 [2] CRAN (R 4.1.0)
## protoclust 1.6.4 2022-04-01 [2] CRAN (R 4.1.2)
## proxy 0.4-27 2022-06-09 [2] CRAN (R 4.1.2)
## ps 1.7.5 2023-04-18 [2] CRAN (R 4.1.2)
## pscl 1.5.5.1 2023-05-10 [2] CRAN (R 4.1.2)
## psych 2.3.6 2023-06-21 [2] CRAN (R 4.1.3)
## pulsar 0.3.10 2023-01-26 [2] CRAN (R 4.1.2)
## purrr * 1.0.1 2023-01-10 [2] CRAN (R 4.1.2)
## qgraph 1.9.5 2023-05-16 [2] CRAN (R 4.1.3)
## quadprog 1.5-8 2019-11-20 [2] CRAN (R 4.1.0)
## qvalue 2.26.0 2021-10-26 [2] Bioconductor
## R6 2.5.1 2021-08-19 [2] CRAN (R 4.1.0)
## RAIDA 1.0 2022-03-14 [2] local
## rbibutils 2.2.13 2023-01-13 [2] CRAN (R 4.1.2)
## RColorBrewer * 1.1-3 2022-04-03 [2] CRAN (R 4.1.2)
## Rcpp * 1.0.11 2023-07-06 [1] CRAN (R 4.1.3)
## RcppZiggurat 0.1.6 2020-10-20 [2] CRAN (R 4.1.0)
## RCurl 1.98-1.12 2023-03-27 [2] CRAN (R 4.1.2)
## Rdpack 2.4 2022-07-20 [2] CRAN (R 4.1.2)
## readr * 2.1.4 2023-02-10 [2] CRAN (R 4.1.2)
## readxl * 1.4.3 2023-07-06 [2] CRAN (R 4.1.3)
## remotes 2.4.2 2021-11-30 [2] CRAN (R 4.1.0)
## reshape2 1.4.4 2020-04-09 [2] CRAN (R 4.1.0)
## reticulate 1.30 2023-06-09 [2] CRAN (R 4.1.3)
## Rfast 2.0.8 2023-07-03 [2] CRAN (R 4.1.3)
## rhdf5 2.38.1 2022-03-10 [2] Bioconductor
## rhdf5filters 1.6.0 2021-10-26 [2] Bioconductor
## Rhdf5lib 1.16.0 2021-10-26 [2] Bioconductor
## rlang 1.1.1 2023-04-28 [1] CRAN (R 4.1.2)
## rmarkdown 2.23 2023-07-01 [2] CRAN (R 4.1.3)
## robustbase 0.99-0 2023-06-16 [2] CRAN (R 4.1.3)
## rootSolve 1.8.2.3 2021-09-29 [2] CRAN (R 4.1.0)
## rpart 4.1.19 2022-10-21 [2] CRAN (R 4.1.2)
## RSpectra 0.16-1 2022-04-24 [2] CRAN (R 4.1.2)
## RSQLite 2.3.1 2023-04-03 [2] CRAN (R 4.1.2)
## rstatix 0.7.2 2023-02-01 [2] CRAN (R 4.1.2)
## rstudioapi 0.15.0 2023-07-07 [2] CRAN (R 4.1.3)
## Rtsne 0.16 2022-04-17 [2] CRAN (R 4.1.2)
## RVenn 1.1.0 2019-07-18 [2] CRAN (R 4.1.0)
## rvest 1.0.3 2022-08-19 [2] CRAN (R 4.1.2)
## S4Vectors * 0.32.4 2022-03-29 [2] Bioconductor
## sandwich 3.0-2 2022-06-15 [2] CRAN (R 4.1.2)
## sass 0.4.6 2023-05-03 [2] CRAN (R 4.1.2)
## scales 1.2.1 2022-08-20 [2] CRAN (R 4.1.2)
## scatterplot3d 0.3-44 2023-05-05 [2] CRAN (R 4.1.2)
## sessioninfo 1.2.2 2021-12-06 [2] CRAN (R 4.1.0)
## sf 1.0-7 2022-03-07 [2] CRAN (R 4.1.2)
## shape 1.4.6 2021-05-19 [2] CRAN (R 4.1.0)
## shiny 1.7.4.1 2023-07-06 [2] CRAN (R 4.1.3)
## sjlabelled 1.2.0 2022-04-10 [2] CRAN (R 4.1.2)
## sjmisc 2.8.9 2021-12-03 [2] CRAN (R 4.1.0)
## snow 0.4-4 2021-10-27 [2] CRAN (R 4.1.0)
## SpiecEasi * 1.1.2 2022-07-14 [2] Github (zdk123/SpiecEasi@c463727)
## SPRING 1.0.4 2022-08-03 [2] Github (GraceYoon/SPRING@3d641a4)
## stringi 1.7.12 2023-01-11 [2] CRAN (R 4.1.2)
## stringr 1.5.0 2022-12-02 [2] CRAN (R 4.1.2)
## SummarizedExperiment * 1.24.0 2021-10-26 [2] Bioconductor
## survival 3.5-5 2023-03-12 [2] CRAN (R 4.1.2)
## svglite 2.1.1 2023-01-10 [2] CRAN (R 4.1.2)
## systemfonts 1.0.4 2022-02-11 [2] CRAN (R 4.1.2)
## tensorA 0.36.2 2020-11-19 [2] CRAN (R 4.1.0)
## TH.data 1.1-2 2023-04-17 [2] CRAN (R 4.1.2)
## tibble * 3.2.1 2023-03-20 [2] CRAN (R 4.1.2)
## tidyr * 1.3.0 2023-01-24 [2] CRAN (R 4.1.2)
## tidyselect 1.2.0 2022-10-10 [2] CRAN (R 4.1.2)
## timechange 0.2.0 2023-01-11 [2] CRAN (R 4.1.2)
## truncnorm 1.0-9 2023-03-20 [2] CRAN (R 4.1.2)
## tzdb 0.4.0 2023-05-12 [2] CRAN (R 4.1.3)
## umap 0.2.10.0 2023-02-01 [2] CRAN (R 4.1.2)
## units 0.8-2 2023-04-27 [2] CRAN (R 4.1.2)
## urlchecker 1.0.1 2021-11-30 [2] CRAN (R 4.1.0)
## usethis * 2.2.2 2023-07-06 [2] CRAN (R 4.1.3)
## utf8 1.2.3 2023-01-31 [2] CRAN (R 4.1.2)
## uuid 1.1-0 2022-04-19 [2] CRAN (R 4.1.2)
## vctrs 0.6.3 2023-06-14 [1] CRAN (R 4.1.3)
## vegan * 2.6-4 2022-10-11 [2] CRAN (R 4.1.2)
## VennDiagram * 1.7.3 2022-04-12 [2] CRAN (R 4.1.2)
## VGAM 1.1-8 2023-03-09 [2] CRAN (R 4.1.2)
## viridis * 0.6.3 2023-05-03 [2] CRAN (R 4.1.2)
## viridisLite * 0.4.2 2023-05-02 [2] CRAN (R 4.1.2)
## vroom 1.6.3 2023-04-28 [2] CRAN (R 4.1.2)
## webshot 0.5.5 2023-06-26 [2] CRAN (R 4.1.3)
## WGCNA 1.72-1 2023-01-18 [2] CRAN (R 4.1.2)
## withr 2.5.0 2022-03-03 [2] CRAN (R 4.1.2)
## Wrench 1.12.0 2021-10-26 [2] Bioconductor
## xfun 0.40 2023-08-09 [1] CRAN (R 4.1.3)
## XMAS2 * 2.2.0 2023-10-27 [1] local
## XML 3.99-0.14 2023-03-19 [2] CRAN (R 4.1.2)
## xml2 1.3.5 2023-07-06 [2] CRAN (R 4.1.3)
## xtable 1.8-4 2019-04-21 [2] CRAN (R 4.1.0)
## XVector 0.34.0 2021-10-26 [2] Bioconductor
## yaml 2.3.7 2023-01-23 [2] CRAN (R 4.1.2)
## zCompositions 1.4.0-1 2022-03-26 [2] CRAN (R 4.1.2)
## zlibbioc 1.40.0 2021-10-26 [2] Bioconductor
## zoo 1.8-12 2023-04-13 [2] CRAN (R 4.1.2)
##
## [1] /Users/zouhua/Library/R/x86_64/4.1/library
## [2] /Library/Frameworks/R.framework/Versions/4.1/Resources/library
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