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BoevaLab / CHIPIN

ChIP-seq Intersample Normalization
GNU General Public License v3.0
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Error when loading hg38 reference genome #2

Closed sgunz closed 3 years ago

sgunz commented 3 years ago

Bug description

When running the following command I get an error message:

CHIPIN_normalize(path_to_bw=pathToFiles, type_norm="quantile", RPKM=pathToRPKMfile, sample_name=sampleName, output_dir=outputFolder, organism="hg38")

Error in CHIPIN_normalize(path_to_bw = bw_path, type_norm = "quantile", : object 'TSS_hg38' not found

Proposed solution

When loading data("TSS_hg38") the resulting dataframe is called hg38TSS instead of TSS_hg38. Changing the following lines in the functions_CHIPIN.R file solved the problem for me.

line 1925: from D_TSS=TSS_hg38 into D_TSS=hg38TSS line 2074: from D_TSS=TSS_hg38 into D_TSS=hg38TSS

Session Info

R version 3.6.3 (2020-02-29) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS 10.16

valeu commented 3 years ago

Thank you Samuel, I have committed this change.