generate_matrix

the path of hic matrix file generated by HiC-Pro, can be found in the ../hic_result/matrix/myhic/iced/resolution/**_iced.matrix

all_hic_file

the path of hic index file generated by HiC-Pro, can be found in the ../hic_result/matrix/myhic/raw/resolution/**_abs.bed

all_bed_file

the picture format of result, if set FALSE, result will be plotted at JPEG format, if TRUE, result will be ploted at PDF format

outputpdf

matrix_dir

chrom_file

generate matrix files from HiC-Pro result
can be used as following command:
generate_matrix(all_hic_file="demo.matrix",all_bed_file="demo.bed",outputpdf="FALSE",matrix_dir="hg19",chrom_file="chrom_hg19.sizes")

 ~kwd1 

 ~kwd2 

Hi-C dataset processing algorithm introduced by Chao He (2016) <doi.org/10.1101/083576>.
The optimized and flexible pipeline for analyzing the
folding of whole chromosome and interactions between some
specific sites from the Hi-C raw sequencing reads to the
partially processed datasets. The other complex genetic and
epigenetic datasets from public sources such as GWAS, ENCODE
consortiums etc. will also easily be integrated into HBP,
hence the final output results of HBP could provide a
comprehensive in-depth understanding for the specific
chromatin interactions, potential molecular mechanisms and
biological significance. We believe that HBP is a reliable
tool for the rapidly analysis of Hi-C data and will be very
useful for a wide range of researchers, particularly those
who lack of background in computational biology.

generate_matrix: generate matrix files

Description

Arguments