MethCORR software

Infer iRNA expression scores for 11 cancer types

MethCORR is an algorithm to calculate inferred RNA (iRNA) expression scores from DNA methylation β-values generated by the Infinium® HumanMethylation450 BeadChip (“450K”).

MethCORR was established by analysis of genome-wide correlations between gene expression and DNA methylation data for eleven cancer types of The Cancer Genome Atlas (TCGA) program.

RNA expression and DNA methylation data was acquired from the UCSC XENA database as “gene expression RNAseq IlluminaHiSeq" and "Methylation450k", respectively.

The included 11 cancer types are:

  • BLAD (Bladder Urothelial Carcinoma)
  • BRCA (Breast Invasive Carcinoma)
  • ESCA (Esophageal Carcinoma)
  • COREAD (Colorectal Adenocarcinoma)
  • LUAD (Lung Adenocarcinoma)
  • LUSC (Lung Squamous Cell Carcinoma)
  • PRAD (Prostate Adenocarcinoma)
  • KIRC (Kidney Renal Clear Cell Carcinoma)
  • SKCM (Skin Cutaneous Melanoma)
  • STAD (Stomach Adenocarcinoma)
  • UCEC (Uterine Corpus Endometrial Carcinoma)

Download R-workspace including example data

MethCORR is distributed as an R workspace encompassing all data objects and scripts needed to calculate iRNA expression scores from any user provided 450K DNA methylation dataset of β-values.
Instructions and example data are included in the download file.

License

The MethCORR software is free for both academic and commercial use. Modification or redistribution of the software is not allowed.
When publishing scientific results, where MethCORR software has been used, please cite the original articles.

Compatibility

MethCORR version 1.00 was developed and tested using R version 4.0.0, the “data.table” R package version 1.12.8 and the “impute” R package version 1.62.0. 

Support

Instructions for use are included with the zip download archive.

If you have any further questions, comments or feedback, we are happy to give e-mail support (within a few days) at bramsen@clin.au.dk.