Nothing
otuCollap <- function(otutab, taxto, siteInCol = TRUE, taxhead='taxonomy', pattern=';', collap=";"){
if (!siteInCol) {
message("Site headers not in columns, will be transposed")
otutab = typeConvert(otutab = data.frame(t(otutab), stringsAsFactors = FALSE), taxhead = taxhead)
}
taxlab = taxhead
colnms = colnames(otutab)
if(!any(grepl(taxlab,colnms))) {
stop(paste0("The input data have not a column named '",taxhead,"'"))
}
taxa = as.vector(otutab[, grepl(taxlab, colnms, ignore.case=TRUE)])
counts = otutab[, !grepl(taxlab, colnms, ignore.case=TRUE)]
taxa = gsub('\\(\\d+\\)','',taxa)
linege = sapply(strsplit(as.character(taxa), split = pattern),
function(x) paste(x[1:taxto],sep='',collapse = collap))
abundance = apply(counts, 2, function(x) tapply(x, INDEX = linege, sum))
Taxonomy = attr(abundance, 'dimnames')[[1]]
result = data.frame(taxonomy = Taxonomy, abundance, stringsAsFactors = FALSE)
rownames(result) = NULL
return(result)
}
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