data: Synthetic datasets used in the package

In ManchesterBioinference/Motif2Site: Detect binding sites from motifs and ChIP-seq experiments, and compare binding sites across conditions

Description

Comparison Yeast synthetic motifs and binding sites: Two synthetic motif files in bed fromat are created to compare them with a synthetic binding site set in terms of precision and recall.

Fur binding sites detection in E. coli build NC_000913: Synthetic Fur ChIp-seq in E. coli was generated using real peaks published in Seo et al 2014. The ChIP-seq data are provided in bed format in fe and dpd condition and both contains two replicates. Synthetic Input ChIP-seq datasets were generated by randomly distributing short reads in E. coli genome. User provided candidate binding sites in bed format was generated by combining instances of "GWWTGANAA" motif with 1-mistmatch and "GWWTGAGAAT" with 2-mismatches in E. coli genome.

Format

Three bed files to compare user provided motifs and binding sites in Yeast. Seven bed files to compare Fur ChIP-seq binding sites in E.coli.

YeastBedFile1.bed

The first synthetic motif set

YeastBedFile2.bed

The second synthetic motif set

YeastSampleMotif.bed

The synthetic binding region

FurMotifs.bed

User provided Fur motif set in E. coli

FUR_fe1.bed

Synthetic Fur ChIP-seq short reads in fe condition rep1

FUR_fe2.bed

Synthetic Fur ChIP-seq short reads in fe condition rep2

FUR_dpd1.bed

Synthetic Fur ChIP-seq short reads in dpd condition rep1

FUR_dpd2.bed

Synthetic Fur ChIP-seq short reads in dpd condition rep2

Input1.bed

The synthetic background Input ChIP-seq rep1

Input2.bed

The synthetic background Input ChIP-seq rep2

Examples

## Data for examplex to compare user provided motifs and binding sites in Yeast 

yeastExampleFile=system.file("extdata", "YeastSampleMotif.bed",
                              package="Motif2Site")
YeastRegionsChIPseq <- Bed2Granges(yeastExampleFile)
bed1 <- system.file("extdata", "YeastBedFile1.bed", package="Motif2Site")
bed2 <- system.file("extdata", "YeastBedFile2.bed", package="Motif2Site")


## Data for examples of binding site detection in E. coli

# FUR candidate motifs in NC_000913 E. coli
FurMotifs = system.file("extdata", "FurMotifs.bed", package="Motif2Site")

# ChIP-seq FUR fe datasets binding sites from user provided bed file 
# ChIP-seq datasets in bed single end format

IPFe <- c(system.file("extdata", "FUR_fe1.bed", package="Motif2Site"),
          system.file("extdata", "FUR_fe2.bed", package="Motif2Site"))


# ChIP-seq FUR dpd datasets binding sites from user provided bed file 
# ChIP-seq datasets in bed single end format

IPDpd <- c(system.file("extdata", "FUR_dpd1.bed", package="Motif2Site"),
           system.file("extdata", "FUR_dpd2.bed", package="Motif2Site"))


# ChIP-seq background

Inputs <- c(system.file("extdata", "Input1.bed", package="Motif2Site"),
            system.file("extdata", "Input2.bed", package="Motif2Site"))

ManchesterBioinference/Motif2Site documentation built on Feb. 13, 2022, 2:03 a.m.