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
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
GRangesListof 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
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
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")
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
install on Travis-ci. However, the package does pass
R CMD check on my own machine.
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