Data Preparation Modules: panoply_sampleqc

panoply_sampleqc

Description

This module assess sample QC using CNA, RNA and proteome data (mapped to gene symbols) based on the following methods (Mertins et al., 2016):

• Sample-level correlation between proteome, RNA, and CNA. Inspecting heatmaps of pairwise correlation between these data types can identify sample swaps or mislabeling
• Co-clustering of RNA and protein data, using only genes with good correlation (> corThreshold). Similarity of sample material used for RNA and protein profiling should result in RNA and protein clustering together for a large fraction of samples
• Comparison of ESTIMATE (Yoshihara et al., 2013) scores for RNA, protein and CNA.

Input

Required inputs:

• tarball: (.tar file) tarball from panoply_harmonize
• type: (String) proteomics data type
• yaml: (.yaml file) parameters in yaml format

Optional inputs:

• corThreshold: (Float, default = 0.4) correlation threshold for filtering genes in RNA and protein data for co-clustering
• outFile: (String, default = "panoply_sampleqc-output.tar") output .tar file name

Output

• outputs Tarball including the following files in the sample-qc subdirectory:
  • ESTIMATE score table for RNA (rna-estimate-scores.gct), CNA (cna-estimate-scores.gct) and proteome (*-estimate-scores.gct)
  • Plots showing correlation heatmaps, co-clustering fanplot and boxplots for ESTIMATE scores (sample-qc-plots.pdf)

References

• Mertins, P., Mani, D., Ruggles, K., Gillette, M., Clauser, K., Wang, P., Wang, X., Qiao, J., Cao, S., Petralia, F., et al. (2016). Proteogenomics connects somatic mutations to signalling in breast cancer. Nature 534(7605), 55 - 62. https://dx.doi.org/10.1038/nature18003.
• Yoshihara, K., Shahmoradgoli, M., nez, E., Vegesna, R., Kim, H., Torres-Garcia, W., o, V., Shen, H., Laird, P., Levine, D., Carter, S., Getz, G., Stemke-Hale, K., Mills, G., Verhaak, R. (2013). Inferring tumour purity and stromal and immune cell admixture from expression data. Nature Communications 4(), 1 - 11. https://dx.doi.org/10.1038/ncomms3612.