| Title: | An example dataset for use with the SVM2CRM package |
|---|---|
| Description: | An example dataset for use with the SVM2CRM package. |
| Authors: | Guidantonio Malagoli Tagliazucchi |
| Maintainer: | Guidantonio Malagoli Tagliazucchi <[email protected]> |
| License: | LGPL (>= 2) |
| Version: | 1.45.1 |
| Built: | 2026-10-10 10:47:49 UTC |
| Source: | https://git.bioconductor.org/packages/SVM2CRMdata |
The first step of the analysis with SVM2CRM is the preprocessing of the data. Basically, SVM2CRM allow to import bed files in the working directory using cisREfindbed. This function import bed files, and then perfomed codify the signals of each histone marks considering the windows size defined by the user. Specially this function require diverse parameters. A vector with the list of bed files that the user want use. The bin.size and the windows size that respectivelly repsent the size of bin used to normalized the data (e.g. 100bp) and windows size that the use want use to describe the signal of each histone marks (e.g. 1000bp). Finally, the user can set a function to smooth the signal of the histone marks inside da particular windows (e.g. median). During this step cisREfindbed generate a data.frame that contains on the column the histone marks, and on the rows the corresponding signals genome-wide.
data(CD4_matrixInputSVMbin100window1000)data(CD4_matrixInputSVMbin100window1000)
A data.frame where in the rows there are the genomic regions while in the columns the signals of histone modifications
see Wang Z et al., 2008
Wang Z, Zang C, Rosenfeld JA, Schones DE, Barski A, Cuddapah S, Cui K, Roh TY,Peng W, Zhang MQ, Zhao K. Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet. 2008 Jul;40(7):897-903.
Histone modification ChIP-seq data in CD4.
"CD4-H2AK5ac.sort.txt""CD4-H2AK5ac.sort.txt"
A bed file
created with a custom script
Wang Z, Zang C, Rosenfeld JA, Schones DE, Barski A, Cuddapah S, Cui K, Roh TY,Peng W, Zhang MQ, Zhao K. Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet. 2008 Jul;40(7):897-903.
Histone modification ChIP-seq data in CD4.
"CD4-H2AK9ac.sort.txt""CD4-H2AK9ac.sort.txt"
A bed file
created with a custom script
Wang Z, Zang C, Rosenfeld JA, Schones DE, Barski A, Cuddapah S, Cui K, Roh TY,Peng W, Zhang MQ, Zhao K. Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet. 2008 Jul;40(7):897-903.
Histone modification ChIP-seq data in CD4.
"CD4-H3K23ac.sort.txt""CD4-H3K23ac.sort.txt"
A bed file
created with a custom script
Wang Z, Zang C, Rosenfeld JA, Schones DE, Barski A, Cuddapah S, Cui K, Roh TY,Peng W, Zhang MQ, Zhao K. Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet. 2008 Jul;40(7):897-903.
Histone modification ChIP-seq data in CD4.
"CD4-H3K27ac.sort.txt""CD4-H3K27ac.sort.txt"
A bed file
created with a custom script
Wang Z, Zang C, Rosenfeld JA, Schones DE, Barski A, Cuddapah S, Cui K, Roh TY,Peng W, Zhang MQ, Zhao K. Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet. 2008 Jul;40(7):897-903.
A bed file of p300 genomic regions.
"GSM393946.distal.p300fromTSS.txt""GSM393946.distal.p300fromTSS.txt"
The output of getSignal
see Wang Z et al., 2008
Wang Z, Zang C, Rosenfeld JA, Schones DE, Barski A, Cuddapah S, Cui K, Roh TY,Peng W, Zhang MQ, Zhao K. Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet. 2008 Jul;40(7):897-903.
Histone modification ChIP-seq data in CD4.
"H3K27me3.sort.txt""H3K27me3.sort.txt"
A bed file
created with a custom script
Wang Z, Zang C, Rosenfeld JA, Schones DE, Barski A, Cuddapah S, Cui K, Roh TY,Peng W, Zhang MQ, Zhao K. Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet. 2008 Jul;40(7):897-903.
Histone modification ChIP-seq data in CD4.
"H3K4me1.sort.txt""H3K4me1.sort.txt"
A bed file
created with a custom script
Wang Z, Zang C, Rosenfeld JA, Schones DE, Barski A, Cuddapah S, Cui K, Roh TY,Peng W, Zhang MQ, Zhao K. Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet. 2008 Jul;40(7):897-903.
Histone modification ChIP-seq data in CD4.
"H3K4me2.sort.txt""H3K4me2.sort.txt"
A bed file
created with a custom script
Wang Z, Zang C, Rosenfeld JA, Schones DE, Barski A, Cuddapah S, Cui K, Roh TY,Peng W, Zhang MQ, Zhao K. Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet. 2008 Jul;40(7):897-903.
Histone modification ChIP-seq data in CD4.
"H3K4me3.sort.txt""H3K4me3.sort.txt"
A bed file
created with a custom script
Wang Z, Zang C, Rosenfeld JA, Schones DE, Barski A, Cuddapah S, Cui K, Roh TY,Peng W, Zhang MQ, Zhao K. Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet. 2008 Jul;40(7):897-903.
This file contain the genomic regions with the p300 binding sites that have a distance of 1000kb from TSSs.
"p300.distal.fromTSS.txt""p300.distal.fromTSS.txt"
A bed file format with chromosome, start, end
see Wang Z et al., 2008
Wang Z, Zang C, Rosenfeld JA, Schones DE, Barski A, Cuddapah S, Cui K, Roh TY,Peng W, Zhang MQ, Zhao K. Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet. 2008 Jul;40(7):897-903.
A bed file with the coordinates of random regions in Hg18, created using a custom script and bedtools (Quinlan AR., et al 2010).
"random.region.hg18.nop300.txt""random.region.hg18.nop300.txt"
A bed file format with chromosome, start, end
created with a custom script
Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010 Mar 15;26(6):841-2.
This dataset contain raw ChIPseq data of H2AK9ac, H3K23ac, H3K27ac, H3K27me3, H3K4me1, H3K4me3 in CD4+ T-cells. Data were downloaded from: Wang Z et al., 2008
Guidantonio Malagoli Tagliazucchi <[email protected]>
dataDir <- system.file("data", package="SVM2CRMdata") setwd(dataDir) dir()dataDir <- system.file("data", package="SVM2CRMdata") setwd(dataDir) dir()
This file contain the output of getSignal using a little number of histone marks and database of random regions without enhancers.
data("train_negative")data("train_negative")
The output of getSignal
see Wang Z et al., 2008
Wang Z, Zang C, Rosenfeld JA, Schones DE, Barski A, Cuddapah S, Cui K, Roh TY,Peng W, Zhang MQ, Zhao K. Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet. 2008 Jul;40(7):897-903.
This file contain the output of getSignal using a little number of histone marks and database of enhancers.
data("train_positive")data("train_positive")
The output of getSignal
see Wang Z et al., 2008
Wang Z, Zang C, Rosenfeld JA, Schones DE, Barski A, Cuddapah S, Cui K, Roh TY,Peng W, Zhang MQ, Zhao K. Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet. 2008 Jul;40(7):897-903.