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GavinHaLab / ichorCNA

Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.
GNU General Public License v3.0
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Change dependency to require R-4.2 #16

Closed ycl6 closed 1 year ago

ycl6 commented 1 year ago

This PR change the required R version to 4.2 to run ichorCNA.

This is due to a bug in GenomeInfoDb to handle hg38 assembly (see #11). The fixed version (v1.34.8) is available in BioC 3.16 (R-4.2). Therefore in order for ichorCNA to work properly when genomeBuild = "hg38", it will also require to run under R-4.2.

I also updated the versions of the imported packages to the version most updated in R-4.2.

ycl6 commented 1 year ago

I have updated the DESCRIPTION to add missing dependencies for data.table and plyr Also the filterEmptyChr function is uncommented so that createPanelOfNormals can be used to create panel of normals.