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Open Source Science

https://github.com/alleninstitute/peakrankr

Package to rank enhancer peaks for cloning

https://github.com/alleninstitute/peakrankr

Science Score: 57.0%

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Last synced: 9 months ago · JSON representation

Repository

Package to rank enhancer peaks for cloning

Basic Info
  • Host: GitHub
  • Owner: AllenInstitute
  • License: other
  • Language: R
  • Default Branch: master
  • Homepage:
  • Size: 10 MB
Statistics
  • Stars: 1
  • Watchers: 2
  • Forks: 0
  • Open Issues: 0
  • Releases: 1
Created about 3 years ago · Last pushed 12 months ago
Metadata Files
Readme License

README.md

DOI

PeakRankR

The R Package can be used to prioritize a list of enahncers/peaks from different groups (e.g. celltypes, subclasses) for cloning and targeting the group of interest. It takes in tsv file with coordinates, group and magnitude (at bare minimum) and two column file (refer below table for sample) listing the bigwig file path and sample id as input and returns the same tsv file with peak ranks calculated per group as output

Required tools to install and run PeakRankR

```

Identiy location of bedtools using:

system("which bedtools")

If not installed please install bedtools using https://bedtools.readthedocs.io/en/latest/content/installation.html

options(bedtools.path = "/path/to/")

bedtoolsr installation

install.packages("devtools") library(devtools) devtools::install_github("PhanstielLab/bedtoolsr")

```

Installation of PeakRanR

``` devtools::install_github("AllenInstitute/PeakRankR", dependencies = T) library(PeakRankR)

```

PeakRankR Algorithm

PeakRankRscore = W(specificity)SpecificityPeak + W(sensitivity)SensitivityPeak +
W(magnitude)MagnitudePeak

where W stands for the weight of each feature. By default each weight variable is set to 1 indicating equal importance for all three features

Running PeakRankR

``` tsvfile <- read.table("testfile.tsv",header=TRUE) # input peaks file with coordinates only/and group name (cell.population) columns (example: testfile.tsv) bwtable <- read.table("bwtable.txt",header=TRUE) # path to bigwig table (example: bwtable)

If group name is given:

Rankedpeaksfile <- PeakRankeR(tsvfiledf = tsvfile, groupbycolumnname = "cell.population", backgroundgroup = unique(tsvfile$"cell.population"), bwtable = bwtable, ranksum = TRUE, weights = c(1,1,1))

```

Note:

  1. In the bwtable file, the sampleid column should match the groupbycolumn_name values

  2. All arguments to the function are mandatory

License

The license for this package is available on Github at: https://github.com/AllenInstitute/PeakRankR/blob/master/LICENSE

Level of Support

We are planning on occasionally updating this repo with no fixed schedule, but likely several times per year. Community involvement is encouraged through both issues and pull requests.

Owner

  • Name: Allen Institute
  • Login: AllenInstitute
  • Kind: organization
  • Location: Seattle, WA

Please visit http://alleninstitute.github.io/ for more information.

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Top Authors
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  • UCDNJJ (2)
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  • SarojaSomu (3)
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Dependencies

DESCRIPTION cran
  • BiocParallel * depends
  • bedtoolsr * depends
  • data.table * depends
  • dplyr * depends
  • tidyr * depends