Commit a99c7108 authored by Christiane Hassenrück's avatar Christiane Hassenrück
Browse files

Merge branch 'master' of gitlab.leibniz-zmt.de:chh/bioinf

parents 78fdf7f8 546fb55a
......@@ -52,8 +52,13 @@ ReadAmplicon <- function(otu, tax, silva, domain,
if (domain == "Bacteria") {
Data0a <- Data0[grep("Bacteria", Tax0$lca_tax_slv), ]
Tax0a <- Tax0[grep("Bacteria", Tax0$lca_tax_slv), ]
Data0b <- Data0a[-c(grep("Chloroplast", Tax0a$lca_tax_slv), grep("mitochondria", Tax0a$lca_tax_slv)), ]
Tax0b <- Tax0a[-c(grep("Chloroplast", Tax0a$lca_tax_slv), grep("mitochondria", Tax0a$lca_tax_slv)), ]
if (length(grep("Chloroplast", Tax0a$lca_tax_slv)) == 0 & length(grep("[Mm]itochondria", Tax0a$lca_tax_slv)) == 0) {
Data0b <- Data0a
Tax0b <- Tax0a
} else {
Data0b <- Data0a[-c(grep("Chloroplast", Tax0a$lca_tax_slv), grep("[Mm]itochondria", Tax0a$lca_tax_slv)), ]
Tax0b <- Tax0a[-c(grep("Chloroplast", Tax0a$lca_tax_slv), grep("[Mm]itochondria", Tax0a$lca_tax_slv)), ]
}
}
if (domain == "Archaea") {
Data0b <- Data0[grep("Archaea", Tax0$lca_tax_slv), ]
......
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