Apply filtering before proceeding with analysis (from yarn paper)

[cgpu]

As highlighted in the current version of the manuscript:

Two types of filtering out must be performed right after the fetching of the gtex.rds via yarn::downloadgtexV8().

• [x] Remove individual GTEX-11ILO - can be done with yarn::checkMisAnnotation()
• [x] Remove outlier cell line

  We excluded K562 from our analyses since this leukemia cell line does not represent a healthy tissue and is only a reference cell line unrelated to any GTEx participants.

• [ ] Exclude genes on sex and mitochondrial chromosomes as they skew the variances

We excluded the X, Y, and mitochondrial genesgenes, and performed PCoA using Euclidean distance on the log2-transformed raw count expression data

[adeslatt]

Didn't see where this was actually done in the code @karleg your assistance here would be greatly appreciated to ensure that we have things in order.

[karleg]

We decided not to merge tissues in the new version

[adeslatt]

@karleg and @pnrobinson could you comment on this :

Exclude genes on sex and mitochondrial chromosomes as they skew the variances
We excluded the X, Y, and mitochondrial genesgenes, and performed PCoA using Euclidean distance on the log2-transformed raw count expression data

We actually don't do this with the gene expression - we do remove the Y chromosome in the differentialSplicingJunctionAnalysis.ipynb but not in the differentialGeneExpressionAnalysis.ipynb

[pnrobinson]

The high variance of the X is biology partially related to the XX v one X, inactivation, escape etc., and so we need to keep it. Differences from the non-PAR regions of the Y are obvious and so we should exclude the Y from all analysis. So far I did not see any difference from the mito,, but there is no reason to exclude it either. We should probably filter out the Y chromosomal results from the DGE result!