chipAnalyseR

An useful R package for ChIP-seq data analysis and visualisation.

!STILL IN DEVELOPMENT!

Installation

devtools::install_github(repo = 'ClaudiaRHD/chipAnalyser')

Usage

What you can do with chipAnalyseR

Visualisation

• Profile plot
• Heat map
  • ordered by row mean average
  • ordered by row mean of one selected matrix
  • clustered by kmeans of one selected matrix
• Peak annotation plotchipAnalyseR::plot_hm(mat = BRD4_mat)
• MA plot
• RNA Polymerase 2 pausing index

Example plots

Profile plot

> BRD4_mat = chipAnalyseR::get_matrix(bed = "GSM2634756_U87_BRD4_peaks.narrowPeak", bw_files = c("GSM2634756_U87_BRD4.bw", "GSM2634758_U87_BRD4_dBET_2h.bw", "GSM2634757_U87_BRD4_dBET_24h.bw"), bw_path = "/R/", op_dir = "/R/GSE99171_RAW/",up = 2500, down = 2500, pos = '', binsize = 10, numcores = 6)
> chipAnalyseR::plot_profile(mat_sum = BRD4_mat, opt = 'mean')

Heat map

> BRD4_mat = chipAnalyseR::get_matrix(bed = "GSM2634756_U87_BRD4_peaks.narrowPeak", bw_files = c("GSM2634756_U87_BRD4.bw", "GSM2634758_U87_BRD4_dBET_2h.bw", "GSM2634757_U87_BRD4_dBET_24h.bw"), bw_path = "/R/", op_dir = "/R/GSE99171_RAW/",up = 2500, down = 2500, pos = '', binsize = 10, numcores = 6)
> chipAnalyseR::plot_hm(mat = BRD4_mat, clusterBy = 'avg')
> chipAnalyseR::plot_hm(mat = BRD4_mat, clusterBy = 1, num_k = 3)

MA plot

> BRD4_auc = chipAnalyseR::auc_pi(bed = "GSM2634756_U87_BRD4_peaks.narrowPeak", bw_files = c("GSM2634756_U87_BRD4.bw", "GSM2634758_U87_BRD4_dBET_2h.bw", "GSM2634757_U87_BRD4_dBET_24h.bw"), bw_path = "/R/", op_dir = "/R/GSE99171_RAW/", numcores = 6)

Peak annotation plot

> chipAnalyseR::peak_annos(p_anno = c("GSM2634756_U87_BRD4_peaks.narrowPeak.anno", "GSM2634758_U87_BRD4_dBET_2h_peaks.narrowPeak.anno"), state2color = "seg.txt")

RNA Polymerase 2 pausing index

> pol2_index = chipAnalyseR::pol2_index(gm = "/media/tempData/claudia/R/sig/hg19_refflat_1k.tsv", bw_files = c("GSM2634756_U87_BRD4.bw", "GSM2634757_U87_BRD4_dBET_24h.bw"), bw_path = "/R/", op_dir = "/R/GSE99171_RAW/", filter = TRUE, numcores = 6 )
> chipAnalyseR::plot_pol2i(pol2_table = pol2_index)