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Last data update: 2014.03.03

R: Perform differential gene expression analysis for mRNA...

getDiffExpressedGenes

R Documentation

Perform differential gene expression analysis for mRNA expression data.

Description

getDiffExpressedGenes returns a list that stores the results for each dataset.

Usage

getDiffExpressedGenes(dataObject, DrawPlots = TRUE, adj.method = "BH",
  adj.pval = 0.05, raw.pval = 0.05, logFC = 2, hmTopUpN = 100,
  hmTopDownN = 100, meanFilter = 10)

Arguments

`dataObject`	This must be `FirehoseData` object.
`DrawPlots`	A logical parameter to draw heatmaps and volcano plots.
`adj.method`	Raw p value adjustment methods (Default "BH")
`adj.pval`	Adjusted p value cut off for results table (Default 0.05)
`raw.pval`	raw p value cut off for results table (Default 0.05)
`logFC`	log fold change cut off for results table (Default 2)
`hmTopUpN`	Max number of up regulated genes in heatmap (Default 100)
`hmTopDownN`	Max number of down regulated genes in heatmap (Default 100)
`meanFilter`	Mean read counts for each gene to filter not expressed genes (Default 10)

Value

Returns a list that stores results for each dataset

Examples

data(RTCGASample)
dgegenes = getDiffExpressedGenes(RTCGASample)
dgegenes
showResults(dgegenes[[1]])
dgegenes = showResults(dgegenes[[1]])
head(dgegenes)
## Not run:

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(RTCGAToolbox)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/RTCGAToolbox/getDiffExpressedGenes.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getDiffExpressedGenes
> ### Title: Perform differential gene expression analysis for mRNA
> ###   expression data.
> ### Aliases: getDiffExpressedGenes
> 
> ### ** Examples
> 
> data(RTCGASample)
RTCGASample dataset is artificially created for function test.
It isn't biologically meaninful and it has no relation with any cancer type.
For real datasets, please use client function to get data from data portal.
> dgegenes = getDiffExpressedGenes(RTCGASample)
> dgegenes
[[1]]
Dataset:RNASeq
DGEResult object, dim: 15	6

> showResults(dgegenes[[1]])
Dataset: RNASeq
          logFC  AveExpr        t      P.Value    adj.P.Val         B
TAP2   5.288573 1.743410 76.38279 7.496531e-76 4.760297e-73 150.82307
GRTP1  6.187648 2.193494 48.25410 2.030875e-60 6.448029e-58 123.44071
ENPP5  7.215676 2.707012 45.79069 1.110692e-58 2.350964e-56 120.11226
APH1B  8.118533 3.158063 37.31744 5.796089e-52 6.134194e-50 106.20724
INSR   8.055541 3.126521 32.82711 7.967149e-48 1.945823e-46  97.36010
MINPP1 7.097777 2.647495 30.36322 2.431258e-45 3.508747e-44  91.95723
> dgegenes = showResults(dgegenes[[1]])
Dataset: RNASeq
          logFC  AveExpr        t      P.Value    adj.P.Val         B
TAP2   5.288573 1.743410 76.38279 7.496531e-76 4.760297e-73 150.82307
GRTP1  6.187648 2.193494 48.25410 2.030875e-60 6.448029e-58 123.44071
ENPP5  7.215676 2.707012 45.79069 1.110692e-58 2.350964e-56 120.11226
APH1B  8.118533 3.158063 37.31744 5.796089e-52 6.134194e-50 106.20724
INSR   8.055541 3.126521 32.82711 7.967149e-48 1.945823e-46  97.36010
MINPP1 7.097777 2.647495 30.36322 2.431258e-45 3.508747e-44  91.95723
> head(dgegenes)
          logFC  AveExpr        t      P.Value    adj.P.Val         B
TAP2   5.288573 1.743410 76.38279 7.496531e-76 4.760297e-73 150.82307
GRTP1  6.187648 2.193494 48.25410 2.030875e-60 6.448029e-58 123.44071
ENPP5  7.215676 2.707012 45.79069 1.110692e-58 2.350964e-56 120.11226
APH1B  8.118533 3.158063 37.31744 5.796089e-52 6.134194e-50 106.20724
INSR   8.055541 3.126521 32.82711 7.967149e-48 1.945823e-46  97.36010
MINPP1 7.097777 2.647495 30.36322 2.431258e-45 3.508747e-44  91.95723
> ## Not run: 
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>