Function visualises time dependent behaviour of genes in two compared groups. The natural cubic spline regression curves fitted to discrete, time dependent expression data are plotted. One plot shows two curves - representing the reference group and the compared group, respectively. See also
number of degrees of freedom
character defining which treatment group should be considered as reference
vector of genes to plot; defalut is
eSetObject must be provided as an object of class
ExpressionSet which contains
Treatment and if applicable
Replicates variables (columns) included in the phenotypic data of the
pData(eSetObject)). Two types of
Treatment defining two groups to compare have to be definied.
Replicates are not required. The time points for compared treatment groups should be identical.
User has to define number of degrees of freedom (
df) for the spline regression model. Choosing effective degrees of freedom in range 3-5 is reasonable.
Genes to plot, given as a vector of characters, can be selected by the user. Provided names have to be a part of a row name vector of
rownames(exprs(eSetObject))). If genes to plot are not definied, all genes are plotted.
A .pdf file containing plots for chosen genes.
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Loading required package: Biobase 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:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colMeans, colSums, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: igraph Attaching package: 'igraph' The following objects are masked from 'package:BiocGenerics': normalize, path, union The following objects are masked from 'package:stats': decompose, spectrum The following object is masked from 'package:base': union Loading required package: limma Attaching package: 'limma' The following object is masked from 'package:BiocGenerics': plotMA Loading required package: GSEABase Loading required package: annotate Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: IRanges Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Loading required package: XML Loading required package: graph Attaching package: 'graph' The following object is masked from 'package:XML': addNode The following objects are masked from 'package:igraph': degree, edges, intersection Loading required package: gtools Attaching package: 'gtools' The following object is masked from 'package:igraph': permute Loading required package: splines Loading required package: GeneNet Loading required package: corpcor Loading required package: longitudinal Loading required package: fdrtool Loading required package: FIs SampleName Time Treatment Replicate 1 T1_1_A 1 T1 A 2 T1_4_A 4 T1 A 3 T1_8_A 8 T1 A 4 T1_16_A 16 T1 A 5 T1_24_A 24 T1 A 6 T1_32_A 32 T1 A 7 T1_40_A 40 T1 A 8 T1_48_A 48 T1 A 9 T1_1_B 1 T1 B 10 T1_4_B 4 T1 B 11 T1_8_B 8 T1 B 12 T1_16_B 16 T1 B 13 T1_24_B 24 T1 B 14 T1_32_B 32 T1 B 15 T1_40_B 40 T1 B 16 T1_48_B 48 T1 B 17 T2_1_A 1 T2 A 18 T2_4_A 4 T2 A 19 T2_8_A 8 T2 A 20 T2_16_A 16 T2 A 21 T2_24_A 24 T2 A 22 T2_32_A 32 T2 A 23 T2_40_A 40 T2 A 24 T2_48_A 48 T2 A 25 T2_1_B 1 T2 B 26 T2_4_B 4 T2 B 27 T2_8_B 8 T2 B 28 T2_16_B 16 T2 B 29 T2_24_B 24 T2 B 30 T2_32_B 32 T2 B 31 T2_40_B 40 T2 B 32 T2_48_B 48 T2 B
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