README.md

In rmflight/fmdatabreastcaparp1: Fondufe-Mittendorfe lab data for PARP1 correlation in MCF-7 and MDA-MB231

Fondufe-Mittendorf Breast Cancer PARP1 Data Package

This package contains the data used for the correlation analysis in the publication:

Genome-wide profiling of PARP1 reveals an interplay with gene regulatory regions and DNA methylation, Nalabothula Narasimharao, Taha Al-jumaily, Robert M. Flight, Shao Xiaorong, Hunter N. B. Moseley, F. Lisa Barcellos, Yvonne Fondufe-Mittendorf, Submitted

This data is used by the correlation analysis package to generate the vignettes that report the actual correlations between PARP1 reads and other data. Unless otherwise noted, all data was downloaded for the MCF-7 cell line.

Please see the vignette for details on sources of data and processing. In most cases, what is done is simply to take data from UCSC and generate a GenomicRanges object that can be worked with in the analysis.

This package contains the following RData objects:

• parp1_ln4_reads_all: all PARP1 reads from MCF-7
• parp1_ln5_reads_all: all PARP1 reads from MDA-MB231
• parp1_ln4_unique: summarized reads, with counts at locations capped at 6
• parp1_ln5_unique: summarized reads, with counts at locations capped at 6
• ctcf_rep1: CTCF ChIP-Seq peaks, replicate 1
• ctcf_rep2: CTCF ChIP-Seq peaks, replicate 2
• methyl_rep1: methylation reads, replicate 1
• methyl_rep2: methylation reads, replicate 2
• histone_marks: GRangesList of ChIP-Seq peaks of various histone marks
• expr_data: Affymetrix HGU-133 2.0 expression data
• tss_windows: 2KB windows around Ensembl transcrip start sites
• nuc_signal: summed MNase nucleosome signal over 500 base tiles of the genome in GM12878

Citation

If this package is used in other analyses, it should be cited as:

fmdatabreastcaparp1: Fondufe-Mittendorfe lab data for PARP1 correlation in MCF-7 and MDA-MB231, R. M. Flight, T. Al-jumaily, Y. Fondufe-Mittendorf, H. N. B. Moseley doi:10.6084/m9.figshare.1267545

Installation

To install this package, you will need to first download the data files from figshare, and then clone this package and install:

git clone https://github.com/rmflight/fmdatabreastcaparp1.git
mkdir fmdatabreastcaparp1/data
wget http://downloads.figshare.com/article/public/1266451.zip
unzip 1266451.zip -d fmdatabreastcaparp1/data

R
library(devtools)
install("fmdatabreastcaparp1")

Notes on Installation and Running Vignette

This package requires a fair amount of memory for the vignette to be run. As far as I can tell, it will need ~4GB to run the part of the vignette that determines what to cap the reads at.

Additionally, I have not been able to do more than a build and install on Travis-ci. However, the package does pass R CMD check on my own machine.

rmflight/fmdatabreastcaparp1 documentation built on May 27, 2019, 9:31 a.m.