This method assigns taxa to the core if they account for some proportion of the total reads for the sequencing run and if they are present in at least x In this example, a core taxa must account for 0.01 for the entire otu table and be present in at least 50
prop_reps(otu_table)
| otu_table | a dataframe of OTUs where the first row is the OTU ID and column names refer to sites |
|---|
the names of OTUs which meet the proportion of replicate criteria
prop_reps(arabidopsis)#> [1] "OTU_10317" "OTU_10942" "OTU_11245" "OTU_11920" "OTU_1196" "OTU_12192" #> [7] "OTU_1274" "OTU_12773" "OTU_12924" "OTU_13052" "OTU_13390" "OTU_14293" #> [13] "OTU_14431" "OTU_14586" "OTU_1460" "OTU_14747" "OTU_14814" "OTU_14818" #> [19] "OTU_14819" "OTU_14820" "OTU_14822" "OTU_14829" "OTU_14834" "OTU_14839" #> [25] "OTU_14939" "OTU_15151" "OTU_15154" "OTU_15169" "OTU_15348" "OTU_15408" #> [31] "OTU_15808" "OTU_15877" "OTU_16467" "OTU_16757" "OTU_16786" "OTU_17465" #> [37] "OTU_18209" "OTU_18240" "OTU_18468" "OTU_18567" "OTU_18761" "OTU_18891" #> [43] "OTU_18923" "OTU_18945" "OTU_18954" "OTU_19047" "OTU_19108" "OTU_19189" #> [49] "OTU_19245" "OTU_19383" "OTU_19482" "OTU_19511" "OTU_19673" "OTU_19706" #> [55] "OTU_19859" "OTU_3106" "OTU_319" "OTU_3327" "OTU_3497" "OTU_3503" #> [61] "OTU_352" "OTU_3613" "OTU_3802" "OTU_3821" "OTU_392" "OTU_4035" #> [67] "OTU_4100" "OTU_5475" "OTU_5635" "OTU_704" "OTU_7054" "OTU_7481" #> [73] "OTU_8660" "OTU_8809" "OTU_9086" "OTU_9309"