Possibility for feature group filtering based on replicate groups and detection frequencies? about patroon

[bhc928]

Hi Rick,

Thanks so much for the quick reply. This makes perfect sense and my apologies for not catching the right section in the manual (I have been scouring the filtering steps/functions...) - unique() and delete() are exactly what I am looking for!

Thanks for the help and have a great day,
Cleo

[rickhelmus]

Hello,

Certainly! There are quite some approaches to delete or select feature groups of interest. The first step is usually to get the names of the feature groups you want to keep or delete.

For instance, in your example were you want to remove all feature groups unique to blanks:

# get a subset of the feature groups that are unique to the blank replicates
fGroupsBlanksUn <- unique(fGroups, which = "blank")
# delete the 'blank features' from the original feature groups
fGroups <- delete(fGroups, j = names(fGroupsBlanksUn))

For more advanced data processing you could first convert the feature group data to a table with as.data.frame()/as.data.table(), filter the table and use the remaining feature group names to subset/delete, e.g.

tab <- as.data.table(fGroups)
# only rows with higher m/z and retention times
tab <- tab[mz > 300 & ret > 200]
fGroupsSub <- fGroups[, tab$group] # subset (ie keep only these)
fGroupsDel <- delete(fGroups, j =  tab$group) # delete (ie remove just these)

More examples are in the handbook ;-)

HTH!
Rick