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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[Documentation Fault]: Poor clarity in DNAm config files #255

Open sof202 opened 5 days ago

sof202 commented 5 days ago

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Fault type

Rewording required

Please describe the fault in detail

According to @lw371, some wording in the two example config files could be fixed up to ensure that users know exactly what we are expecting from them.

config.txt

It should be clear that the path to Rconfig needs the file name at the end (“config.r”)

config.r

Maybe make it clearer that all project variables you want coloured have to be included in “projVar” and that they should exactly match the headings in your sampleSheet file

Explain the QC thresholds more?