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Last data update: 2014.03.03

R: Exploration of expression data.

Data_Exploration

R Documentation

Exploration of expression data.

Description

Take the expression data and the feature annotations to generate the results that will be used for the exploratory plots (explo.plot) or saved by the user to perform other analyses.

Usage

dat(input, type = c("biodetection","cd","countsbio","GCbias","lengthbias","saturation","PCA"), 
                    k = 0, ndepth = 6, factor = NULL, norm = FALSE, refColumn = 1, logtransf = FALSE)

Arguments

`input`	Object of eSet class with expression data and optional annotation.
`type`	Type of plot for which the data are to be generated. It can be one of: "biodetection","cd","countsbio","GCbias","lengthbias","saturation".
`k`	A feature is considered to be detected if the corresponding number of read counts is > k. By default, k = 0. This parameter is used by types "biodetection" and "saturation".
`ndepth`	Number of different sequencing depths to be simulated and plotted apart from the real depth. By default, ndepth = 6. This parameter is only used by type "saturation".
`factor`	If factor = NULL (default), the calculations are done for each sample independently. When the factor is specified, the calculations are done for each experimental condition. Samples within the same condition are summed up ("biodetection") or averaged and normalized by sequencing depth ("countsbio", "GCbias" and "lengthbias").
`norm`	To indicate if provided data are already normalized (TRUE) or they are raw data (FALSE), which is the default. This parameter is used by types "cd", "lengthbias", "GCbias" and "countsbio".
`refColumn`	Column number in input data that is taken as the reference sample to compute M values. This parameter is only used by type "cd".
`logtransf`	To indicate if the data are already log-transformed (TRUE) or not (FALSE). If data are not log-transformed, a log-transformation will be applied before computing the Principal Component Analysis.

Value

dat() function returns an S4 object to be used by explo.plot() or to be converted into a more friendly formatted object by the dat2save() function.

Author(s)

Sonia Tarazona

Examples

## Load the input object with the expression data and the annotations
data(myCounts)

## Generating data for the plot "biodetection" and samples in columns 3 and 4 of expression data
mydata2plot = dat(mydata, type = "biodetection", k = 0)

## Generating the corresponding plot
explo.plot(mydata2plot, samples = c(3,4))

Results


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(NOISeq)
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: splines
Loading required package: Matrix
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/NOISeq/dat.Rd_%03d_medium.png", width=480, height=480)
> ### Name: Data_Exploration
> ### Title: Exploration of expression data.
> ### Aliases: dat
> 
> ### ** Examples
> 
> ## Load the input object with the expression data and the annotations
> data(myCounts)
> 
> ## Generating data for the plot "biodetection" and samples in columns 3 and 4 of expression data
> mydata2plot = dat(mydata, type = "biodetection", k = 0)
Biotypes detection is to be computed for:
 [1] "R1L1Kidney" "R1L2Liver"  "R1L3Kidney" "R1L4Liver"  "R1L6Liver" 
 [6] "R1L7Kidney" "R1L8Liver"  "R2L2Kidney" "R2L3Liver"  "R2L6Kidney"
> 
> ## Generating the corresponding plot
> explo.plot(mydata2plot, samples = c(3,4))
Warning messages:
1: In if (plottype == "persample") { :
  the condition has length > 1 and only the first element will be used
2: In if (plottype == "comparison") { :
  the condition has length > 1 and only the first element will be used
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>