A class generated from the function computeDEGs() containing the result of the differential expression analysis at the two expression levels.
Slots
DEGs.table:
Object of class matrix containing all the differential expression analysis. The matrix contains one row for each gene, while columns are organized as follows:
log2 FC(1st level), log2 fold change in the first level,
avg(1st level,control), average signal intensities of the control samples in the first level,
sd(1st level,control), standard deviation of the signal intensities of the control samples in the first level,
avg(1st level,treated), average signal intensities of the treated samples in the first level,
sd(1st level,treated), standard deviation of the signal intensities of the treated samples in the first level,
pv.METHOD(1st level), the differential expression p-value returned from the chosen method in the first level (the name of this column will change according to the selected method),
pv.METHOD.BH(1st level), the Benjamini-Hochberg corrected differential expression p-value returned from the chosen method in the first level (the name of this column will change according to the selected method),
log2 FC(2nd level), log2 fold change in the second level,
avg(2nd level,control), average signal intensities of the control samples in the second level,
sd(2nd level,control), standard deviation of the signal intensities of the control samples in the second level,
avg(2nd level,treated), average signal intensities of the treated samples in the second level,
sd(2nd level,treated), standard deviation of the signal intensities of the treated samples in the second level,
pv.METHOD(2nd level), the differential expression p-value returned from the chosen method in the second level (the name of this column will change according to the selected method),
pv.METHOD.BH(2nd level), the Benjamini-Hochberg corrected differential expression p-value returned from the chosen method in the second level (the name of this column will change according to the selected method),
level1Up, boolean value set to 1 if the gene is upregulated in the first level, otherwise set to 0,
level1Down, boolean value set to 1 if the gene is downregulated in the first level, otherwise set to 0,
level2Up, boolean value set to 1 if the gene is upregulated in the second level, otherwise set to 0,
level2Down, boolean value set to 1 if the gene is downregulated in the second level, otherwise set to 0,
DownDown, boolean value set to 1 if the gene is downregulated in both levels, otherwise set to 0,
DownUp, boolean value set to 1 if the gene is downregulated in the first level and up regulated in the second level, otherwise set to 0,
UpDown, boolean value set to 1 if the gene is upregulated in the first level and downregulated in the second level, otherwise set to 0,
UpUp, boolean value set to 1 if the gene is upregulated in both levels, otherwise set to 0
method:
Object of class character specifying the statistical method used to detect DEGs.
significance.threshold:
Object of class numeric specifying the significance threshold used to detect DEGs.
FC.threshold:
Object of class numeric specifying the fold change threshold used to detect DEGs.
label.level.DEGs:
Object of class character specifying the names of the two levels compared in the experiment.
label.condition:
Object of class character specifying the names of the two conditions compared in the experiment.
Accessors
getDEGsMethod
signature(object = "DEGs"): displays an object of class character specifying the statistical method used to detect DEGs.
significance.threshold
signature(object = "DEGs"): displays an object of class numeric specifying the significance threshold used to detect DEGs.
FC.threshold
signature(object = "DEGs"): displays an object of class numeric specifying the fold change threshold used to detect DEGs.
label.level.DEGs
signature(object = "DEGs"): displays an object of class character specifying the names of the two levels compared in the experiment.
label.condition
signature(object = "DEGs"): displays an object of class character specifying the names of the two conditions compared in the experiment.
DEGs.table
signature(object = "DEGs"): displays an object of class matrix specifying the table of computed DEGs.
Methods
CVplot
signature(object = "DEGs"): enables the generation of a plot where, for each level, signal coefficients of variation for each gene are displayed against their log2 fold changes. DEGs are color labeled.
GOEnrichment
signature(object = "DEGs"): enables the GO enrichment analysis of the differentially expressed genes at each level.
RegulatoryEnrichment
signature(object = "DEGs"): enables the enrichment analysis of post-transcriptional regulators (RBPs, miRNAs, ecc) in the DEGs gene list, by means of Fisher test.
Histogram
signature(object = "DEGs"): enables the generation of a histogram displaying the number of DEGs belonging to different classes according to their expression behaviour at the two levels.
MAplot
signature(object = "DEGs"): enables the generation of a plot where, for each level, average signal intensities for each gene are displayed against their log2 fold changes. DEGs are color labeled.
Scatterplot
signature(object = "DEGs"): enables the generation of a plot where fold changes at the first level are displayed for each gene against fold changes at the second level. DEGs are color labeled.
SDplot
signature(object = "DEGs"): enables the generation of a plot where, for each level, signal standard deviations for each gene are displayed against their log2 fold changes. DEGs are color labeled.
show
signature(object = "DEGs"): displays all the six slots of the class.
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(tRanslatome)
Loading required package: limma
Loading required package: sigPathway
Loading required package: samr
Loading required package: impute
Loading required package: matrixStats
matrixStats v0.50.2 (2016-04-24) successfully loaded. See ?matrixStats for help.
Loading required package: anota
Loading required package: qvalue
Loading required package: DESeq
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 object is masked from 'package:limma':
plotMA
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, 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, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
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 objects are masked from 'package:matrixStats':
anyMissing, rowMedians
Loading required package: locfit
locfit 1.5-9.1 2013-03-22
Loading required package: lattice
Welcome to 'DESeq'. For improved performance, usability and
functionality, please consider migrating to 'DESeq2'.
Loading required package: edgeR
Loading required package: RankProd
Loading required package: topGO
Loading required package: graph
Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: SparseM
Attaching package: 'SparseM'
The following object is masked from 'package:base':
backsolve
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
Attaching package: 'topGO'
The following object is masked from 'package:IRanges':
members
Loading required package: org.Hs.eg.db
Loading required package: GOSemSim
Loading required package: Heatplus
Loading required package: gplots
Attaching package: 'gplots'
The following object is masked from 'package:IRanges':
space
The following object is masked from 'package:S4Vectors':
space
The following object is masked from 'package:stats':
lowess
Loading required package: plotrix
Attaching package: 'plotrix'
The following object is masked from 'package:gplots':
plotCI
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/tRanslatome/DEGs.Rd_%03d_medium.png", width=480, height=480)
> ### Name: DEGs-class
> ### Title: Class 'DEGs'
> ### Aliases: DEGs-class CVplot,DEGs-method DEGs.table,DEGs-method
> ### FC.threshold,DEGs-method RegulatoryEnrichment,DEGs-method
> ### GOEnrichment,DEGs-method Histogram,DEGs-method
> ### label.condition,DEGs-method label.level.DEGs,DEGs-method
> ### MAplot,DEGs-method getDEGsMethod,DEGs-method Scatterplot,DEGs-method
> ### SDplot,DEGs-method show,DEGs-method
> ### significance.threshold,DEGs-method
> ### Keywords: classes DEGs differential expression
>
> ### ** Examples
>
> showClass("DEGs")
Class "DEGs" [package "tRanslatome"]
Slots:
Name: DEGs.table method significance.threshold
Class: matrix character numeric
Name: FC.threshold label.level.DEGs label.condition
Class: numeric character character
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.