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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Remove tech var and bio var variables #220

Closed ew367 closed 1 month ago

ew367 commented 1 month ago

Description

This pull request will remove the techVar and bioVar variables from the config.example.r,  checkRconfigFile.r and QC.rmd files and replace them with an overal projVar (project variable).

It will also hard code Sentrix_ID and Sentrix_Position into the QC.rmd doc plots.

Issue ticket number

This pull request is to address issues: #33, #188 and #216

Type of pull request

Checklist

sof202 commented 1 month ago

As long as the stuff I've pointed out aren't problems. This is functional and is an improvement over using bioVar and techVar.

sof202 commented 1 month ago

This also fixes a problem I had with the define_plot_parameters function where it would output blank vectors if bioVar and techVar were empty. Thank you