A R wrapper for qgrs-cpp. The latter is a C++ implementation of QGRS mapping algorithm published by freezer333 on https://github.com/freezer333/qgrs-cpp. This project support a R wrapper that allow analysis possible G4 structures in transcript from a specific gene list. It also provide a executable file of qgrs-cpp on win64.
The original papers:
- Frees, S., Crum, M., Menendez, C., Bagga, P.S. (2014) "QGRS-Conserve: A Computational Method for Discovering Evolutionarily Conserved G-quadruplex Motifs". Human Genetics, BioMed Central, Vol 8 (8)
- Menendez, C., Frees, S., and Bagga, P. (2012) QGRS-H Predictor: A Web Server for Predicting Homologous Quadruplex forming G-Rich Sequence Motifs in Nucleotide Sequences. Nucleic Acids Res. doi: 10.1093/nar/gks42240: W96-W103.
Rscript G4_analysis.R [regionType] [gene.csv] [qgrs_exec_filepath]
The code has been tested on Windows.
The following command line options are supported:
regionType: fiveUTR, threeUTR, cds
gene.csv: input file, example in gene.csv
qgrs_exec_filepath: qgrs executable file path, default is The built-in qgrs executable, please specific it if it not work
By default, output is in res folder, temporary files is in tmp folder. The implication of column are showed on column titles, the last 8 columns are the output for qgrs-cpp, please refer to https://github.com/freezer333/qgrs-cpp for more informations.
library(GenomicRanges)
library(BSgenome.Hsapiens.UCSC.hg38)
library(TxDb.Hsapiens.UCSC.hg38.knownGene)
library(org.Hs.eg.db)
library(dplyr)