── Attaching packages ─────────────────────────────────────── tidyverse 1.3.0 ── ✔ ggplot2 3.3.2 ✔ purrr 0.3.4 ✔ tibble 3.0.4 ✔ dplyr 1.0.2 ✔ tidyr 1.1.2 ✔ stringr 1.4.0 ✔ readr 1.4.0 ✔ forcats 0.5.0 ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ── ✖ dplyr::filter() masks stats::filter() ✖ dplyr::lag() masks stats::lag() Loading required package: S4Vectors Loading required package: stats4 Loading required package: BiocGenerics Loading required package: parallel Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:parallel’: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from ‘package:dplyr’: combine, intersect, setdiff, union The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Attaching package: ‘S4Vectors’ The following objects are masked from ‘package:dplyr’: first, rename The following object is masked from ‘package:tidyr’: expand The following object is masked from ‘package:base’: expand.grid Loading required package: IRanges Attaching package: ‘IRanges’ The following objects are masked from ‘package:dplyr’: collapse, desc, slice The following object is masked from ‘package:purrr’: reduce Loading required package: GenomicRanges Loading required package: GenomeInfoDb Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: ‘matrixStats’ The following object is masked from ‘package:dplyr’: count Attaching package: ‘MatrixGenerics’ The following objects are masked from ‘package:matrixStats’: colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: ‘Biobase’ The following object is masked from ‘package:MatrixGenerics’: rowMedians The following objects are masked from ‘package:matrixStats’: anyMissing, rowMedians converting counts to integer mode seqname source feature start end score strand frame 1 ##gff-version 3 NA NA 2 1 FIG CDS 1 1368 . + 1 3 1 FIG CDS 1379 2479 . + 2 4 1 FIG CDS 2485 3567 . + 1 5 1 FIG CDS 3631 4776 . - 1 6 1 FIG CDS 4813 5616 . - 1 att 1 2 ID=fig|729.2200.peg.1;Name=Chromosomal replication initiator protein DnaA 3 ID=fig|729.2200.peg.2;Name=DNA polymerase III beta subunit (EC 2.7.7.7);Ontology_term=KEGG_ENZYME:2.7.7.7 4 ID=fig|729.2200.peg.3;Name=DNA recombination and repair protein RecF 5 ID=fig|729.2200.peg.4;Name=N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25);Ontology_term=KEGG_ENZYME:3.5.1.25 6 ID=fig|729.2200.peg.5;Name=Glucosamine-6-phosphate deaminase (EC 3.5.99.6);Ontology_term=KEGG_ENZYME:3.5.99.6 seqname source feature start end score strand frame 1 1 FIG CDS 138 1231 . + 1 2 1 FIG CDS 1489 2369 . + 2 3 1 FIG CDS 2593 3459 . + 1 4 1 FIG CDS 3746 4662 . - 1 5 1 FIG CDS 4893 5536 . - 1 6 1 FIG CDS 5795 6497 . - 1 att 1 ID=fig|729.2200.peg.1;Name=Chromosomal replication initiator protein DnaA 2 ID=fig|729.2200.peg.2;Name=DNA polymerase III beta subunit (EC 2.7.7.7);Ontology_term=KEGG_ENZYME:2.7.7.7 3 ID=fig|729.2200.peg.3;Name=DNA recombination and repair protein RecF 4 ID=fig|729.2200.peg.4;Name=N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25);Ontology_term=KEGG_ENZYME:3.5.1.25 5 ID=fig|729.2200.peg.5;Name=Glucosamine-6-phosphate deaminase (EC 3.5.99.6);Ontology_term=KEGG_ENZYME:3.5.99.6 6 ID=fig|729.2200.peg.6;Name=N-acetylneuraminate lyase (EC 4.1.3.3);Ontology_term=KEGG_ENZYME:4.1.3.3 [1] "Generating pseudo-datasets" [1] 1 Joining, by = "Pos" [1] 2 Joining, by = "Pos" [1] 3 Joining, by = "Pos" [1] 4 Joining, by = "Pos" [1] 5 Joining, by = "Pos" [1] 6 Joining, by = "Pos" [1] 7 Joining, by = "Pos" [1] 8 Joining, by = "Pos" [1] 9 Joining, by 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Joining, by = "Pos" [1] 941 Joining, by = "Pos" [1] 942 Joining, by = "Pos" [1] 943 Joining, by = "Pos" [1] 944 Joining, by = "Pos" [1] 945 Joining, by = "Pos" [1] 946 Joining, by = "Pos" [1] 947 Joining, by = "Pos" [1] 948 Joining, by = "Pos" [1] 949 Joining, by = "Pos" [1] 950 Joining, by = "Pos" [1] 951 Joining, by = "Pos" [1] 952 Joining, by = "Pos" [1] 953 Joining, by = "Pos" [1] 954 Joining, by = "Pos" [1] 955 Joining, by = "Pos" [1] 956 Joining, by = "Pos" [1] 957 Joining, by = "Pos" [1] 958 Joining, by = "Pos" [1] 959 Joining, by = "Pos" [1] 960 Joining, by = "Pos" [1] 961 Joining, by = "Pos" [1] 962 Joining, by = "Pos" [1] 963 Joining, by = "Pos" [1] 964 Joining, by = "Pos" [1] 965 Joining, by = "Pos" [1] 966 Joining, by = "Pos" [1] 967 Joining, by = "Pos" [1] 968 Joining, by = "Pos" [1] 969 Joining, by = "Pos" [1] 970 Joining, by = "Pos" [1] 971 Joining, by = "Pos" [1] 972 Joining, by = "Pos" [1] 973 Joining, by = "Pos" [1] 974 Joining, by = "Pos" [1] 975 Joining, by = "Pos" [1] 976 Joining, by = "Pos" [1] 977 Joining, by = "Pos" [1] 978 Joining, by = "Pos" [1] 979 Joining, by = "Pos" [1] 980 Joining, by = "Pos" [1] 981 Joining, by = "Pos" [1] 982 Joining, by = "Pos" [1] 983 Joining, by = "Pos" [1] 984 Joining, by = "Pos" [1] 985 Joining, by = "Pos" [1] 986 Joining, by = "Pos" [1] 987 Joining, by = "Pos" [1] 988 Joining, by = "Pos" [1] 989 Joining, by = "Pos" [1] 990 Joining, by = "Pos" [1] 991 Joining, by = "Pos" [1] 992 Joining, by = "Pos" [1] 993 Joining, by = "Pos" [1] 994 Joining, by = "Pos" [1] 995 Joining, by = "Pos" [1] 996 Joining, by = "Pos" [1] 997 Joining, by = "Pos" [1] 998 Joining, by = "Pos" [1] 999 Joining, by = "Pos" [1] 1000 Joining, by = "Pos" [1] "Binning read counts by gene boundaries" converting counts to integer mode Warning message: In DESeqDataSet(se, design = design, ignoreRank) : some variables in design formula are characters, converting to factors gene-wise dispersion estimates mean-dispersion relationship -- note: fitType='parametric', but the dispersion trend was not well captured by the function: y = a/x + b, and a local regression fit was automatically substituted. specify fitType='local' or 'mean' to avoid this message next time. final dispersion estimates log2 fold change (MLE): condition Hp305 vs Expected Wald test p-value: condition Hp305 vs Expected DataFrame with 6 rows and 6 columns baseMean log2FoldChange lfcSE stat pvalue padj 2 1.028246 3.381280 0.272022 12.430165 1.79264e-35 5.20635e-33 3 0.997349 -3.149959 0.845402 -3.725988 1.94551e-04 1.12562e-03 4 970.287890 -2.043397 0.979652 -2.085840 3.69932e-02 1.09472e-01 5 1443.150870 -2.220240 0.813454 -2.729397 6.34502e-03 2.43845e-02 6 1699.046420 -2.119660 0.730271 -2.902564 3.70121e-03 1.52011e-02 7 1076.618681 -0.274546 0.911880 -0.301076 7.63356e-01 9.02269e-01 Package 'mclust' version 5.4.6 Type 'citation("mclust")' for citing this R package in publications. Attaching package: ‘mclust’ The following object is masked from ‘package:purrr’: map ---------------------------------------------------- Gaussian finite mixture model fitted by EM algorithm ---------------------------------------------------- Mclust V (univariate, unequal variance) model with 2 components: log-likelihood n df BIC ICL -4004.495 2033 5 -8047.077 -8863.05 Clustering table: 1 2 892 1141 Mixing probabilities: 1 2 0.5369784 0.4630216 Means: 1 2 -2.5511037 -0.4078168 Variances: 1 2 4.9452213 0.4259998 ------------------------------------------------------- Density estimation via Gaussian finite mixture modeling ------------------------------------------------------- Mclust V (univariate, unequal variance) model with 2 components: log-likelihood n df BIC ICL -4004.496 2033 5 -8047.078 -8862.959 null device 1 [1] "Unchanged" "Reduced" "Reduced" "Reduced" "Reduced" "Unchanged" [7] "Unchanged" "Reduced" "Reduced" "Unchanged" converting counts to integer mode Warning message: In DESeqDataSet(se, design = design, ignoreRank) : some variables in design formula are characters, converting to factors gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates log2 fold change (MAP): condition Hp305 vs Expected Wald test p-value: condition Hp305 vs Expected DataFrame with 6 rows and 6 columns baseMean log2FoldChange lfcSE stat pvalue padj 2 1.028246 3.336119 0.268762 12.412932 2.22358e-35 6.45791e-33 3 0.997349 -2.816815 0.684098 -4.117560 3.82904e-05 3.02897e-04 4 970.287890 -1.704624 0.832133 -2.048499 4.05111e-02 1.30937e-01 5 1443.150870 -1.958660 0.724851 -2.702156 6.88914e-03 3.45818e-02 6 1699.046420 -1.917343 0.664780 -2.884176 3.92440e-03 2.14470e-02 7 1076.618681 -0.237583 0.790483 -0.300554 7.63755e-01 9.02740e-01 ---------------------------------------------------- Gaussian finite mixture model fitted by EM algorithm ---------------------------------------------------- Mclust X (univariate normal) model with 1 component: log-likelihood n df BIC ICL -3236.591 2033 2 -6488.416 -6488.416 Clustering table: 1 2033 Mixing probabilities: 1 1 Means: [1] -1.059624 Variances: [1] 1.413653 ------------------------------------------------------- Density estimation via Gaussian finite mixture modeling ------------------------------------------------------- Mclust X (univariate normal) model with 1 component: log-likelihood n df BIC ICL -3236.591 2033 2 -6488.416 -6488.416 null device 1 [1] "Unchanged" "Reduced" "Reduced" "Reduced" "Reduced" "Reduced" [7] "Reduced" "Reduced" "Reduced" "Unchanged"