hicproraw-to-bedpe

Import a HiC-Pro raw .matrix and .bed of any resolution into R and generate a .bedpe.Rds object.

Description

HiC-Pro raw matrices are in a sparse upper-triangular format, however they are output as two plain text files: a .matrix and a .bed

The hicpro2bedpe function from HiCcompare is used in this module to produce a sparse upper-triangular matrix in BEDPE format, which is required as input by multiHiCCompare.

References

• multiHiCcompare vignette

Acknowledgements

• This SO post exemplifying how to save an object when its name is in a string variable was originally used, however saveRDS() was later favoured.

Author

Helena Reyes Gopar