Show method for phyloCompData object.
# S4 method for class 'phyloCompData'
show(object)mydata <- generateSyntheticData(dataset = "mydata", n.vars = 1000,
samples.per.cond = 5, n.diffexp = 100,
id.species = factor(1:10),
tree = ape::rphylo(10, 1, 0),
lengths.relmeans = "auto", lengths.dispersions = "auto")
#> Warning: `id.species` is not named. I'm naming them, assuming they are in the same order as the tree.
mydata
#> An object of class phyloCompData
#> Dataset name: mydata
#> Number of samples: 10
#> Number of variables: 1000
#> Number of random outliers: 0
#> Number of single outliers: 0
#> Number of known truly differentially expressed genes: 100
#> No differential expression analysis has been performed.
#>
#> count.matrix:
#> t1 t2 t3 t4 t5 t6
#> g1 1506 3952 2715 2499 2661 1836
#> g2 1823 7875 5712 5490 3051 13929
#> g3 8514 3713 4691 4685 2096 7309
#> g4 44 112 82 62 101 211
#> g5 87 61 93 28 104 54
#> g6 6699 9267 33917 5055 6282 21129
#> + 994 rows and 4 cols...
#>
#> sample.annotations:
#> condition depth.factor id.species id.condition
#> t1 1 1.370978 1 1
#> t2 1 1.307948 2 1
#> t3 1 1.200042 3 1
#> t4 1 1.132634 4 1
#> t5 1 1.242833 5 1
#> t6 2 1.399927 6 2
#> + 4 rows...
#>
#> variable.annotations:
#> truedispersions.S1 truedispersions.S2 truemeans.S1 truemeans.S2
#> g1 0.09260841 0.09260841 263.097561 417.439792
#> g2 0.06393425 0.06393425 549.736842 947.000378
#> g3 0.14710871 0.14710871 198.731707 309.770686
#> g4 0.33036219 0.33036219 6.195122 16.937126
#> g5 0.32619725 0.32619725 4.146341 6.583614
#> g6 0.05951280 0.05951280 444.195122 1453.798986
#> n.random.outliers.up.S1 n.random.outliers.up.S2 n.random.outliers.down.S1
#> g1 0 0 0
#> g2 0 0 0
#> g3 0 0 0
#> g4 0 0 0
#> g5 0 0 0
#> g6 0 0 0
#> n.random.outliers.down.S2 n.single.outliers.up.S1 n.single.outliers.up.S2
#> g1 0 0 0
#> g2 0 0 0
#> g3 0 0 0
#> g4 0 0 0
#> g5 0 0 0
#> g6 0 0 0
#> n.single.outliers.down.S1 n.single.outliers.down.S2 M.value A.value
#> g1 0 0 0.6201669 11.636430
#> g2 0 0 1.1276886 12.625310
#> g3 0 0 0.5435606 12.350101
#> g4 0 0 0.8198613 6.678071
#> g5 0 0 0.2411374 6.227492
#> g6 0 0 1.0824596 13.723640
#> truelog2foldchanges upregulation downregulation differential.expression
#> g1 0.6659703 1 0 1
#> g2 0.7846238 1 0 1
#> g3 0.6403786 1 0 1
#> g4 1.4509845 1 0 1
#> g5 0.6670408 1 0 1
#> g6 1.7105623 1 0 1
#> prop.var.tree lengths.relmeans lengths.dispersions M.value.TPM A.value.TPM
#> g1 1 2849.071 0.8967967 0.06744422 1.3099313
#> g2 1 2445.857 1.3552594 0.45138422 2.7912837
#> g3 1 3449.571 0.4941060 0.48983533 0.7316052
#> g4 1 2175.357 0.1358132 1.25335505 -4.1621203
#> g5 1 2753.643 0.7451979 1.02926846 -5.8166748
#> g6 1 2989.929 1.0779904 1.76041101 2.7067230
#> + 994 rows...
#>
#> Phylogenetic tree:
#>
#> Phylogenetic tree with 10 tips and 9 internal nodes.
#>
#> Tip labels:
#> t1, t2, t3, t4, t5, t6, ...
#>
#> Rooted; includes branch length(s).
#>
#> length.matrix:
#> t1 t2 t3 t4 t5 t6
#> g1 469 1111 1204 1029 1953 573
#> g2 306 1371 962 930 492 1238
#> g3 6378 3100 2687 2942 1686 2586
#> g4 1423 2008 3794 2016 1890 1383
#> g5 8459 5414 6084 3037 5856 1134
#> g6 1573 2339 8468 1922 1944 1601
#>