Calculate QC Metrics for Taxa and Samples
calculateQC(x)A phyloseq object
A list with two tibbles.
SampleQC
sample_total_taxa:Total taxa in a sample
sample_total_reads:Total reads in a sample
number_taxa_account_fifty_percent:Number of taxa account for 50 percent
TaxaQC
taxa_counts:Total counts of taxa in all samples
taxa_mean_counts:Mean counts of taxa in all samples
taxa_dectected_samples:Number of samples in which taxa detected
taxa_prevalence:Percent of samples in which taxa detected
Calculate QC metrics for taxa and samples.
library(biomeUtils)
data("FuentesIliGutData")
qc_Data <- calculateQC(FuentesIliGutData)
qc_Data
#> $SampleQC
#> # A tibble: 589 × 4
#> Samples sample_total_taxa sample_total_reads number_taxa_account_fifty_pe…¹
#> <chr> <dbl> <dbl> <int>
#> 1 sample_1 259 15237 11
#> 2 sample_2 291 18970 16
#> 3 sample_3 336 21161 16
#> 4 sample_4 355 17754 20
#> 5 sample_5 300 25724 11
#> 6 sample_6 374 33815 14
#> 7 sample_7 251 13810 15
#> 8 sample_8 273 22730 15
#> 9 sample_9 279 22706 15
#> 10 sample_10 219 15521 9
#> # … with 579 more rows, and abbreviated variable name
#> # ¹number_taxa_account_fifty_percent
#>
#> $TaxaQC
#> # A tibble: 905 × 9
#> taxa taxa_counts taxa_me…¹ taxa_…² taxa_cv taxa_…³ taxa_…⁴ taxa_…⁵ perce…⁶
#> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 ASV302 13913 23.6 47.3 2.00 648 504 85.6 4.44e-2
#> 2 ASV636 4063 6.90 27.4 3.97 462 112 19.0 1.30e-2
#> 3 ASV500 6223 10.6 45.0 4.26 535 227 38.5 1.98e-2
#> 4 ASV7 784128 1331. 1652. 1.24 899 578 98.1 2.50e+0
#> 5 ASV2617 311 0.528 1.50 2.84 45 117 19.9 9.92e-4
#> 6 ASV148 40396 68.6 224. 3.26 765 189 32.1 1.29e-1
#> 7 ASV196 24796 42.1 137. 3.26 724 248 42.1 7.91e-2
#> 8 ASV2699 294 0.499 1.81 3.63 40.5 68 11.5 9.38e-4
#> 9 ASV109 60088 102. 303. 2.97 798 454 77.1 1.92e-1
#> 10 ASV1472 907 1.54 3.62 2.35 229 197 33.4 2.89e-3
#> # … with 895 more rows, and abbreviated variable names ¹taxa_mean_counts,
#> # ²taxa_stdev_counts, ³taxa_rank, ⁴taxa_dectected_samples, ⁵taxa_prevalence,
#> # ⁶percent_of_total
#>