Aldex.clr object subsetting description

[K-Pimentel]

I have been using aldex.clr on subsets of my data to compare different conditions in my experiment. However, it would seem to make more sense to run aldex.clr on the whole dataset and then subset the transformed data to compare the selected conditions.

It seems that this should be possible looking at the aldex.clr-class description but the description in the vignette for the package is unclear/contains errors(?):

numMCInstances(x): Returns the names of the keys that can be used to subset the data rows. The keys values are the rsid’s. This returns a single number not names?

getFeatureNames(x): Returns the names of the keys that can be used to subset the data rows. The keys values are the rsid’s. This seems to be the correct use of this descriptor which is repeated for all the access functions

getReads(x): Returns the names of the keys that can be used to subset the data rows. The keys values are the rsid’s. This seems to be a repeat of the former descriptor

numConditions(x): Returns the names of the keys that can be used to subset the data rows. The keys values are the rsid’s. This returns a number not a name?

getMonteCarloReplicate(x, i): Returns the names of the keys that can be used to subset the data rows. The keys values are the rsid’s. This returns a single number, the number of Monte Carlo replicates.... is this an error?

Is it is possible to use the values of for example 'sample IDs' or '@conds' to select samples of interest?

[elayton13]

Did you ever figure this out? I am also confused about how to subset my data and do the pairwise comparisons

[RachBioHaz]

Ditto - ended up working from subsets