rlbps: R-loop Binding Proteins

In Bishop-Laboratory/RLHub: An ExperimentHub package for accessing processed RLSuite data sets

Description

A list of annotations for genomic features relevant to R-loops. Both mm10 and hg38 annotations are available.

Usage

rlbps(quiet = FALSE)

Arguments

quiet

If TRUE, messages are suppressed. Default: FALSE.

Details

Source

R-Loop binding proteins (RLBPs) are proteins which were discovered by mass-spectrometry after S9.6 immuno-precipitation (S9.6 is an antibody that binds R-loops). The data were aggregated from three studies which analyzed RLBPs in this manner:

1. Nadel et al., 2015 - article

2. Wang et al., 2018 - article

3. Cristini et al., 2018 - article

The data were downloaded from the supplementary materials of each study and processed using custom R scripts as part of the RLBase-data pipeline. This processing involved normalization of mass-spec abundance calculations and the derivation of a "combined score" for ranking all the proteins.

Structure

geneName	NADEL.2015	WANG.2018	CRISTINI.2018	combinedScore
DDX21	0.9	0	0.968	1.87
DHX9	0.85	0.0635	0.831	1.74
...	...	...	...	...

Columns:

• geneName

  • The official HGNC symbol of the RLBP

• NADEL.2015

  • Normalized abundance of protein from Nadel et al., 2015

• WANG.2018

  • Normalized abundance of protein from Wang et al., 2018

• CRISTINI.2018

  • Normalized abundance of protein from Cristini et al., 2018

• combinedScore

  • Sum of normalized abundance across studies.

Value

A tbl object. See details.

Examples

rlbpsData <- rlbps()

Bishop-Laboratory/RLHub documentation built on Jan. 20, 2022, 3:47 p.m.