README for dptscan (0.7.x)

Introduction

dptscan implements the iDPT method(2), which integrates signal Deconvolution, whole genome Pattern recognition and scan, and differential Testing into a consolidated pipeline, to address the group-wise comparison of genome-wide, enrichment-based profiles generated by massively parallel sequencing. dptscan project website: http://idpt.github.com/dptscan/

Requirement

• Linux servers (recommend multicore servers with > 128G memory)
• R 2.14 or greater with RScript installed. R packages required: MCMCpack, nlme, gmodels, MASS, plyr, preprocessCore, inline, Rcpp, IRanges, Biostrings, mmap, getopt, snowfall, multicore, qvalue.

Installation

• Follow Data preparation and Profile binning steps.
• Create a project folder. Copy the binned profile data to the data input subfolder, InputData (default).
• Download the dptscan zipball and unzip the files into the project folder. Make dptscan executable with chmod +x dptscan.
• Modify samplesheet.text and experiment-config.r files.
• Initiate the workspace with

dptscan -s

Usage

dptscan [options]

Example:

dptscan --batch=1,1,5,5,5 --core=1,10,4,4,4

Options:

--verbose	Show more on-screen information.
-s	Setup dptscan workspace.
--task=TASK	Select one or more modules from "preprocess", "mixPoi", "pattRecog", "diffTest", "report". DEFAULT: "preprocess, mixPoi, pattRecog, diffTest, report", which applies the complete dpscan process with all the modules in a proper order.
--chr=CHR	Select one or a set of chromosomes to run. DEFAULT:1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y,M, which processes on all the chromosomes.
--core=CORE	Number of computer cores used in parallel for each batch.
--batch=BATCH	Number of batch tasks in parallel.
--samplesheet=file	Sample sheet file. DEFAULT: "samplesheet.txt".
--config=CONFIG	Configuration file for running parameters.DEFAULT: "experiment-config.r".
--output=PATH	Path to output result files. DEFAULT: "./", current location.
--analysis=methyl	Analysis category. DEFAULT: methyl, DNA methylation analysis.

Reference

1. Xu Y, Hu B, Choi AJ, Gopalan B, Lee BH, Kalady MF, Church JM, and Ting AH. Unique DNA methylome profiles in CpG island methylator phenotype colon cancers. Genome Res 2012, Feb;22(2):283-91.
2. Ting AH, Hu B, Zhang L, Na J, Lee BH, and Xu Y. iDPT: an integrative approach for de novo identification of differentially enriched events in multi-sample sequencing studies (under review).