R: Heatmap that represent the fold changes of all the five...
inHeatmap
R Documentation
Heatmap that represent the fold changes of all the five features
Description
Heatmap that represent the fold changes of all the five features
A method to see as an heatmap the logRatios of synthesis, degradation and processing rates and
pre-mRNA and total mRNA concentration of a population of genes, either at the level of
etimated or modeled rates.
Eiher "pre-model" or "model" to switch between pre-modeled or modeled features
breaks
A vector of breaks for the heatmap
palette
A color generating function, output of colorRampPalette
plot_matureRNA
A logical. If set to TRUE, matrue-mRNA is displayed instead of
total-mRNA (default: FALSE)
absoluteExpression
A logical. If set to FALSE, the plot representing the
intensity of expression is omitted. (default=TRUE)
rowLabels
A character that represent the label names that will be
shown on the y-axis of the heatmap. If NULL featureNames(object) will be shown
(default is NULL)
clustering
A logical. If set to FALSE, it displys genes the order they are,
with no clustering (default: TRUE)
clustIdx
A numeric. Indicates which of the features are used for the
clustering. 0=absoluteExpression; 1=total-mRNA/mature-mRNA; 2=preMRNA;
3=synthesis; 4=degradation; 5=processing (default=3:5, meaning that
synthesis, degradation and processing are used for the clustering)
Value
A list of matrices containing the logRatios for total mRNA levels, pre-mRNA levels,
synthesis rates, degradation rates and processing rates. Matrices are ordered according to
the clustering.
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(INSPEcT)
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, 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
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: BiocParallel
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/INSPEcT/inHeatmap.Rd_%03d_medium.png", width=480, height=480)
> ### Name: inHeatmap
> ### Title: Heatmap that represent the fold changes of all the five features
> ### Aliases: inHeatmap inHeatmap,INSPEcT-method
>
> ### ** Examples
>
> data('mycerIds10', package='INSPEcT')
> inHeatmap(mycerIds10, 'pre-model')
> inHeatmap(mycerIds10, 'model')
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.
