Chapter 4 Data processing
Loading packages
library(XMAS2)
library(dplyr)
library(tibble)
library(phyloseq)This part has too may procedures and we only choose some of them. Please go to XMAS tutorial: Chapter 6 to see more approaches and details for being familiar with this part.
4.1 Rarefy otu counts
From previous results of quality evaluation, the sequence depth of samples are different which have effects on the downstream analysis. Here, choosing the rarefy (Normaliztion method: random subsampling counts to the smallest library size) to get the equal sample sums.
dada2_ps_rare <- norm_rarefy(object = dada2_ps_remove_BRS,
size = 51181)
dada2_ps_rare## phyloseq-class experiment-level object
## otu_table() OTU Table: [ 891 taxa and 23 samples ]
## sample_data() Sample Data: [ 23 samples by 1 sample variables ]
## tax_table() Taxonomy Table: [ 891 taxa by 7 taxonomic ranks ]
## phy_tree() Phylogenetic Tree: [ 891 tips and 888 internal nodes ]
## refseq() DNAStringSet: [ 891 reference sequences ]In addition, we could also perform some other normalization methods on the rarefied phyloseq object. By the way, we didn’t transform the data by using log algorithm because the count matrix is required by the following data analysis methods.
4.2 Extracting specific taxonomic level
dada2_ps_rare_genus <- summarize_taxa(ps = dada2_ps_rare,
taxa_level = "Genus")
dada2_ps_rare_genus## phyloseq-class experiment-level object
## otu_table() OTU Table: [ 198 taxa and 23 samples ]
## sample_data() Sample Data: [ 23 samples by 1 sample variables ]
## tax_table() Taxonomy Table: [ 198 taxa by 6 taxonomic ranks ]4.3 Systematic Information
devtools::session_info()## ─ Session info ──────────────────────────────────────────────────────────────────────────────────────────────────────────────
## setting value
## version R version 4.1.2 (2021-11-01)
## 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 2022-08-09
## rstudio 2022.07.1+554 Spotted Wakerobin (desktop)
## pandoc 2.18 @ /Applications/RStudio.app/Contents/MacOS/quarto/bin/tools/ (via rmarkdown)
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