Run a correlation between genetic distance and gene expression & methylation distance matrices

[AHuffmyer]

1) generate a distance matrix (Bray Curtis or another method?) for genetic distance (done), gene expression distance, and methylation distance for pairwise sample comparisons 2) run a correlation of genetic distance to gene expression distance and genetic distance to methylation distance 3) plot the relationships 4) proceed with RDA if desired

[sr320]

genetic distance matrix https://github.com/sr320/ceabigr/blob/main/output/53-revisit-epi-SNPs/epiMATRIX_mbd_rab.txt

[kubu4]

RNAseq gene distance matrix:

CSV: https://github.com/sr320/ceabigr/blob/main/output/52.1-rnaseq-relatedness/gene-distance-matrix.csv

Code: https://github.com/sr320/ceabigr/blob/main/code/52.1-rnaseq-relatedness.Rmd

Heatmap: https://github.com/sr320/ceabigr/blob/main/output/52.1-rnaseq-relatedness/figures/gene-distance-matrix-heatmap.pdf

Heatmap:

[sr320]

@kubu4 can we get this matrix where we have specific sample IDs?

[kubu4]

Done! Thanks for the catch. Didn't realize write.csv() couldn't keep column/row names; switched to write.table() instead.