TRAPR: R package for statistical analysis and visualization of RNA-Seq data

Jae Hyun Lim , Soo Youn Lee , Ju Han Kim *

Abstract: RNA-Seq, is a standard technology for measuring gene expression at an unprecedented accuracy. Numerous Bioconductor packages have been developed for statistical analysis of RNA-Seq data. However, those tools focus on specific aspects of the data analysis pipeline and are hard to integrate appropriately with each other because of their ununified data structure and processing methods. They also lack visualization methods to confirm data integrity and process. Here, we present an R based RNA-Seq analysis pipeline TRAPR, an integrated tool including statistical analysis and visualization of RNA-Seq expression data. TRAPR provides various functions for data management, filtering of low quality data, normalization, transformation, statistical analysis, data visualization, and result visualization that allow researchers to build customized analysis pipelines.TRAPR is written in R (as of version 2.15.1 )


Download TRAPR Source Code

Download TRAPR Package for linux

Download TRAPR Package for Mac os

Download TRAPR User's Guide

Download TRAPR R Reference Manual

What's TRAPR?

TRAPR is R based RNA-Seq analysis pipeline. Fig0 present RNA-seq data analysis pipeline of TRAPR.

Fig0. RNA-seq data analysis pipeline of TRAPR.


1 Set up TRAPR package in your R

2 Previous set up packages

3 Loading TRAPR package

4 Format of input file

5 Sample data

6 Start TRAPR analysis

  6.1 Data Manipulation

  6.2 Filter

  6.3 Normalization

  6.4 Data Visualization

  6.5 Statistical Test

  6.6 Result Visualization

  6.7 Out-print of DEG Result file

* Our manual was made based on window 7

1 Set up TRAPR package in your R
Download TRAPR package and install

2. Previous set up packages
TRAPR must be needs some R packages(vsn, preprocessCore, edgeR, gridExtra, ggplot2, reshape2). We will show description of package setup method. For example, we explain vsn.

Fig1 Dependent packages installation

> biocLite('vsn')
> biocLite('preprocessCore')
> biocLite('gridExtra')
> biocLite('ggplot2')
> biocLite('reshape2')

3. Loading TRAPR package

> library(TRAPR)

4. Format of input file
TRAPR input file consist of Tab-deliminated text file. Column is sample list. Row is gene list. Each cell is filled gene expression values(Fig2).

Fig2. input format of TRAPR

5. Sample data
Our sample data file name is 'sample.txt'. This file contained in TRAPR. The origin of sample.txt is breast cancer data from TCGA. It consist of 9 normal tissue cancer sample and 10 cancer sample using RNA-seq technology and ItӬ?s value is FPKM(Fig3).

Fig3 sample.txt in TRAPR

6. Start TRAPR analysis
6.1 Data Manipulation

> Sample <- TRAPR.Data.ReadExpressionTable('sample.txt', sep = '\t', Exp1 = c(1:9), Exp2 = c(10:19), Tag = c('Normal', 'Cancer'))

Function loading sample file is TRAPR.Data.ReadExpressionTable. The code component explain showing Fig3. More Information in reference manual.
Fig4 sample loading code & example

Sample position (green color) is description for sample column position. Tag (blue color) is description for sample labels. Loaded sample data is saving 'Sample' value and after using function of filtering and normalization. More Information in reference manual.

6.2 Filter

Fig5 Zero value filtering function code & example

6.3 Normalization

Fig6 Normalization function code & example

6.4 Data Visualization

Fig7 Data visualization function code & example

Fig8 Result example plot of data visualization

6.5 Statistical Test

TRAPR provide 4 method for statistical test ('ttest', 'wilcoxon', 'edgeR', 'FC'). If you needs another function, just write method name replace ' ttest '(purple color). TRAPR also provide adjust test method('holm', 'hotchberg', 'hommel', 'bonferroni', 'BH', 'BY', 'fdr', 'none').

Fig9 Result visualization function code & example

6.6 Result Visualization
TRAPR provide Result plot of after statistical test. We provide 2 kinds of plots (Heatmap, volcano plot)(Fig11).

Fig11 Result example plot of result visualization

Fig11 Result example plot of result visualization

6.7 Out-print of DEG Result file
TRPR provide out-print your DEG result file in your directory. User just typing file name(blue color) in code.

Fig12 Out-print of DEG Result file function code & example