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 677 464 623 540 994 1244
#> g2 212 91 136 469 38 320
#> g3 8650 3501 5651 10353 5132 20182
#> g4 2244 918 1921 786 3791 12941
#> g5 1408 2153 3537 2927 1555 4067
#> g6 19796 23016 32019 12395 49297 34190
#> + 994 rows and 4 cols...
#>
#> sample.annotations:
#> condition depth.factor id.species id.condition
#> t1 1 1.1059100 1 1
#> t2 1 0.8032296 2 1
#> t3 1 1.1182325 3 1
#> t4 1 1.1147645 4 1
#> t5 1 1.3286844 5 1
#> t6 2 0.8657358 6 2
#> + 4 rows...
#>
#> variable.annotations:
#> truedispersions.S1 truedispersions.S2 truemeans.S1 truemeans.S2
#> g1 0.06746282 0.06746282 91.07018 186.80398
#> g2 0.35363024 0.35363024 20.24390 41.06688
#> g3 0.10650664 0.10650664 249.17544 793.82092
#> g4 0.22208438 0.22208438 39.14634 206.19044
#> g5 0.11717587 0.11717587 229.14634 504.91998
#> g6 0.08663472 0.08663472 464.22807 933.00555
#> 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 0.9084921 9.659980
#> g2 0 0 1.5140718 7.742311
#> g3 0 0 1.7738109 13.371876
#> g4 0 0 2.1714704 11.652939
#> g5 0 0 1.1464079 11.550079
#> g6 0 0 0.6879611 14.816299
#> truelog2foldchanges upregulation downregulation differential.expression
#> g1 1.036475 1 0 1
#> g2 1.020488 1 0 1
#> g3 1.671652 1 0 1
#> g4 2.397028 1 0 1
#> g5 1.139786 1 0 1
#> g6 1.007052 1 0 1
#> prop.var.tree lengths.relmeans lengths.dispersions M.value.TPM A.value.TPM
#> g1 1 1048.357 0.002140625 0.9137434 -0.3109954
#> g2 1 3344.571 1.012137002 0.8081918 -2.6379876
#> g3 1 5960.214 0.295973014 1.4061421 1.3670502
#> g4 1 5180.857 0.239087670 2.4666154 -0.6862882
#> g5 1 3419.000 0.468503762 1.0678868 0.7691664
#> g6 1 6651.714 0.257245838 1.1252715 1.7610089
#> + 994 rows...
#>
#> Phylogenetic tree:
#>
#> Phylogenetic tree with 10 tips and 9 internal nodes.
#>
#> Tip labels:
#> t1, t2, t3, t4, t5, t6, ...
#>
#> Rooted; includes branch lengths.
#>
#> length.matrix:
#> t1 t2 t3 t4 t5 t6
#> g1 1017 966 969 1004 1033 948
#> g2 1352 797 675 3133 522 1478
#> g3 4357 2609 3214 5569 2928 5110
#> g4 5965 5802 6721 3340 7706 8664
#> g5 1001 2301 2408 2868 889 1723
#> g6 8443 10457 10574 5099 19246 7769
#>