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mervesa / HiCDCPlus

HiCDCPlus
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There is no "file_out=TRUE" in hic2icenorm_gi_list function #12

Closed TingtingSsl2 closed 2 years ago

TingtingSsl2 commented 2 years ago

Dear HiCDCPlus developers,

I'm using hic2icenorm_gi_list before finding TADs. The instruction (https://github.com/mervesa/HiCDCPlus) says that there is file_out=TRUE option to output normalized data. "You can also output a ICE normalized .hic file from hic2icenorm_gi_list function if you set file_out=TRUE with the name of gsub(".hic","_icenorm.hic",hic_path)."

However, the help page found only hic_output and this hic_output can only direct output to the input file folder, not to customized location. I'm wondering if you can help with this confusion.

Bests,

Tingting

mervesa commented 2 years ago

Hello @TingtingSsl2 , you are correct and the README is misleading in that it gives an appearance of custom file outputs while the only output path available is gsub(".hic","_icenorm.hic",hic_path) when one indicates hic_output=TRUE. I have corrected the README files accordingly. Thank you very much!

mervesa commented 2 years ago

Hi, I've just pushed the changes to the vignette here and to Bioconductor's current release. The most timely way to use the changes would be to reinstall the package using devtools : library(devtools); install_github("mervesa/HiCDCPlus")