10/30/2022 0 Comments 16s rdna sequence analysisWrite.table(ps1 %>% transform_sample_counts( function(x) ) %>% psmelt() %>% select(Genus, Sample_ID, Abundance) %>% spread(Sample_ID, Abundance), file = "outfiles/expr.relative_", sep = " \t ", quote = F, row.names = F, col.names = T) Write.table(ps1 %>% psmelt() %>% arrange(OTU) %>% rename( ASV = OTU) %>% select(ASV, Kingdom, Phylum, Class, Order, Family, Genus, Species, Sample_ID, Abundance) %>% spread(Sample_ID, Abundance), file = "outfiles/", sep = " \t ", quote = F, row.names = F, col.names = T) write.table(ps1 %>% tax_glom( taxrank = "Phylum") %>% psmelt() %>% select(Phylum, Sample_ID, Abundance) %>% spread(Sample_ID, Abundance), file = "outfiles/", sep = " \t ", quote = F, row.names = F, col.names = T) write.table(ps1 %>% tax_glom( taxrank = "Class") %>% psmelt() %>% select(Class, Sample_ID, Abundance) %>% spread(Sample_ID, Abundance), file = "outfiles/", sep = " \t ", quote = F, row.names = F, col.names = T) write.table(ps1 %>% tax_glom( taxrank = "Family") %>% psmelt() %>% select(Family, Sample_ID, Abundance) %>% spread(Sample_ID, Abundance), file = "outfiles/", sep = " \t ", quote = F, row.names = F, col.names = T) write.table(ps1 %>% tax_glom( taxrank = "Genus") %>% psmelt() %>% select(Genus, Sample_ID, Abundance) %>% spread(Sample_ID, Abundance), file = "outfiles/", sep = " \t ", quote = F, row.names = F, col.names = T) # Species TaxaID SampleID count RelativeAbundance # 844452: Bacteria Firmicutes Clostridia Oscillospirales Ruminococcaceae Subdoligranulum # 844451: Bacteria Firmicutes Clostridia Oscillospirales Ruminococcaceae Subdoligranulum # 844450: Bacteria Firmicutes Clostridia Oscillospirales Ruminococcaceae Subdoligranulum # 844449: Bacteria Firmicutes Clostridia Oscillospirales Ruminococcaceae Subdoligranulum # 844448: Bacteria Firmicutes Clostridia Oscillospirales Ruminococcaceae Subdoligranulum Mdt = fast_melt(ps0) mdt # Kingdom Phylum Class Order Family Genus # 6702: Bacteria Firmicutes Clostridia Oscillospirales Ruminococcaceae Subdoligranulum # 6701: Bacteria Firmicutes Clostridia Oscillospirales Ruminococcaceae Subdoligranulum # 6700: Bacteria Firmicutes Clostridia Oscillospirales Ruminococcaceae Subdoligranulum # 6699: Bacteria Firmicutes Clostridia Oscillospirales Ruminococcaceae Subdoligranulum # 6698: Bacteria Firmicutes Clostridia Oscillospirales Ruminococcaceae Subdoligranulum # 5: Bacteria Firmicutes Clostridia Oscillospirales Ruminococcaceae Subdoligranulum # 4: Bacteria Firmicutes Clostridia Oscillospirales Ruminococcaceae Subdoligranulum # 3: Bacteria Firmicutes Clostridia Oscillospirales Ruminococcaceae Subdoligranulum # 2: Bacteria Firmicutes Clostridia Oscillospirales Ruminococcaceae Subdoligranulum # 1: Bacteria Firmicutes Clostridia Oscillospirales Ruminococcaceae Subdoligranulum Tdt = data.table( setDT( as.ame( tax_table(ps0))), TotalCounts = taxa_sums(ps0), SV = taxa_names(ps0)) tdt # Kingdom Phylum Class Order Family Genus
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