Not a problem, but a couple of feature request

[nmb85]

Hi, Mads,

Great tool; much thanks! Could you add a function to segregate out by pps taxon (or marker gene taxon), such as:

function(df, name, level, omit = F) { name <- paste(toupper(substring(name,1,1)), substring(name,2,), sep = "") level <- tolower(level) new_df <- list(scaffolds = data.frame(), essential = data.frame()) if (omit == F) { eval(parse(text = paste("newdf$scaffolds <- df$scaffolds[df$scaffolds$pps", level, " == \"", name,"\", ]", sep = ""))) } else if (omit == T) { eval(parse(text = paste("newdf$scaffolds <- df$scaffolds[df$scaffolds$pps", level, " != \"", name,"\", ]", sep = ""))) } else { message("The \"omit\" value should be either True or False") stop() } new_df$scaffolds <- new_df$scaffolds[is.na(new_df$scaffolds$scaffold) == F, ] new_df$essential <- df$essential[df$essential$scaffold %in% new_df$scaffolds$scaffold, ] return(new_df) }

Also, could you add a function to slice the list of dataframes by coverage?

I find myself doing both things quite frequently...

[MadsAlbertsen]

Thanks for the good suggestions - I'll look into it.

[MadsAlbertsen]

Reopened to make sure I remember it.

[MadsAlbertsen]

I've added a generic mmsubset function (It simply wraps the default "subset" function in R). It should be included in the 0.5.0 version.

It should be able to subset based on the function you describe - if I understood it correctly.

data(rocco)
d_gc60 <- mmsubset(data = d, gc > 60)
d_Actinobacteria <- mmsubset(data = d, pps_phylum == "Actinobacteria")

[nmb85]

Looks fantastic! Very useful; thank you!