Hi- I used OneCodex to do WGS on mouse fecal samples, and processed the data on their platform through the HUMAnN3 program. In comparing the pathways identified between my three study groups (control n=5 independent mice; treatment #1 n=5 independent mice; treatment #2 n=7 independent mice) there are 233 pathways that are commonly expressed in all 3 groups. I would like to statistically compare the total abundance (RPK) of each of the 233 pathways between the 3 groups to see which comparisons are significantly different.
Because there are overlaps in the genes shared amongst the 233 pathways (identified by MetaCyc pathway ID), a biostatistician suggested that I first do orthogonality filtering for the HUMAnN pathways to narrow the list of 233 pathways down to those that contain unique gene sets and maintain more power in my analysis. After doing that, for the remaining pathways I would run a one-way ANOVA with post hoc bonferroni or FDR correction.
Does a script already exist for orthogonality filtering for Humann pathways? Any advice or help on this would be much appreciated! Thank you in advance.