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ejh243 / BrainFANS

Complex Disease Epigenomics Group's quality control and analysis pipelines for DNA methylation arrays, SNP arrays, BS-Seq, ATAC-Seq and ChIP-Seq
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[Bug]: `cellType` is not defined in CETYGOdeconvolution.R #183

Closed sof202 closed 2 months ago

sof202 commented 2 months ago

What happened?

cellType is not being set prior to the call:

paste0(dataDir, "/2_gds/QCmetrics/CETYGO/CETYGOscorePlots_", cellType, ".pdf")

As such the script will fail here, resulting in the 2_gds/QCmetrics/CETYGO/ directory being empty after 1_runDNAmQC.sh is ran.

How can the bug be reproduced?

Run CETYGOdeconvolution.r on any dataset and config file.

sof202 commented 2 months ago

I've got it wrong. An error is cropping up related to cell type, but this is not the cause of it.