ChIPSeeker peaks plotting and summarizing script

R script to run the ChIPSeeker peak annotation and summary plotting pipeline on .bed files.

[ Example output files can be seen here ]

[ Example report output can be seen here]

To run the basic script on selected files:

./peak-summary.R /path/to/Sample1_peaks.bed /path/to/Sample2_peaks.bed 

To compile a report on a directory of files:

./compile-peak-type-summary-report.R -d example-data

• -d, --dir: Dir mode; treat input items as directories in which to search for .bed files
• -id-dirname: Use the directory name of each input file as the sample ID, instead of the filename
• --out-dir: Parent directory to save the output to
• --tss-dist: TSS region distance

Annotate & plot .bed files

$ ./peak-summary.R example-data/Sample1.bed example-data/Sample2.bed

Annotate all .bed files in a directory, and save results to a different output directory

$ ./peak-summary.R example-data/ -d --out-dir example-output

• Tested with R version 3.2.3 and 3.3.0, with the following packages:
  • ChIPseeker_1.6.7
  • clusterProfiler_2.4.3
  • TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
  • optparse_1.3.2