Extra 'simplify' parameter needed in subset_metabarlist

[grossebusedu38]

subset_metabarlist <- function(metabarlist, table, indices)

would become

subset_metabarlist <- function(metabarlist, table, indices, simplify=TRUE)

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when simplify=FALSE, do not remove any columns in the reads table:

reads <- reads[, colSums(reads) > 0, drop = F]

would become

reads <- reads[, (colSums(reads) > 0) & simplify, drop = F]

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usefull when you want to compare the reads table of two subseted metabarlist that were originally the same:

Example:

soil_euk2 <- soil_euk
soil_euk2$reads <- corrected

metabaR::ggpcrtag(soil_euk2)
metabaR::ggpcrtag(soil_euk)

s1<- subset_metabarlist(soil_euk, 'pcrs', {v <- soil_euk$pcrs$control_type=="sequencing";v[is.na(v)]<-F;v})
s2 <- subset_metabarlist(soil_euk2, 'pcrs', {v <- soil_euk$pcrs$control_type=="sequencing";v[is.na(v)]<-F;v})

s(1|2)$reads and s(1|2)$motus tables are not easily comparable