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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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[Enhancement suggestion]: Remove techVar and bioVar variables and replace with hardcoded Sentrix_ID and Sentrix_Position and optional project variables (projVar) #216

Closed ew367 closed 1 month ago

ew367 commented 2 months ago

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Enhancement suggestion

Remove techVar and bioVar variables and replace with hardcoded Sentrix_ID and Sentrix_Position and optional project variables (projVar)

Sentrix_ID and Sentrix_Position will need to be included as plot variables in the QC report for all projects so should be hardcoded in to the QC.rmd script. There is also no need to distinguish between technical and biological variables so these can be combined into an overall (optional) project variable.

affected scripts:

config.example.r,  checkRconfigFile.r and QC.rmd files

ew367 commented 2 months ago

This also address #188

sof202 commented 1 month ago

Also addresses #33 I think