tests/testthat/_snaps/edgeR.md
In yiluheihei/microbiomeMarker: microbiome biomarker analysis toolkit
result of edger
Code
print(marker_table(mm_edger), digits = 5)
Output
feature
marker1 k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria
marker2 k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales
marker3 k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales|f__Enterobacteriaceae
marker4 k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales|f__Enterobacteriaceae|g__Klebsiella
marker5 k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales|f__Enterobacteriaceae|g__Klebsiella|g__Klebsiella_s__
marker6 k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales|f__Enterobacteriaceae|g__Escherichia
marker7 k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales|f__Enterobacteriaceae|g__Escherichia|s__coli
marker8 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__adolescentis
marker9 k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__[Paraprevotellaceae]|g__Paraprevotella
marker10 k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__[Paraprevotellaceae]|g__Paraprevotella|g__Paraprevotella_s__
marker11 k__Bacteria|p__Proteobacteria
marker12 k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Roseburia
marker13 k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Roseburia|g__Roseburia_s__
marker14 k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Clostridiaceae|f__Clostridiaceae_g__Clostridium|f__Clostridiaceae_g__Clostridium_s__
marker15 k__Bacteria|p__Cyanobacteria|c__4C0d-2
marker16 k__Bacteria|p__Cyanobacteria|c__4C0d-2|o__YS2
marker17 k__Bacteria|p__Cyanobacteria|c__4C0d-2|o__YS2|o__YS2_f__
marker18 k__Bacteria|p__Cyanobacteria|c__4C0d-2|o__YS2|o__YS2_f__|o__YS2_f___g__
marker19 k__Bacteria|p__Cyanobacteria|c__4C0d-2|o__YS2|o__YS2_f__|o__YS2_f___g__|o__YS2_f___g___s__
marker20 k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rickettsiales|f__mitochondria
marker21 k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rickettsiales|f__mitochondria|f__mitochondria_g__
marker22 k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rickettsiales|f__mitochondria|f__mitochondria_g__|f__mitochondria_g___s__
marker23 k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rickettsiales
marker24 k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|g__Prevotella_s__
marker25 k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria
marker26 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Bifidobacteriales
marker27 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Bifidobacteriales|f__Bifidobacteriaceae
marker28 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Actinomycetales
marker29 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium
marker30 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Actinomycetales|f__Nocardioidaceae
marker31 k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__[Paraprevotellaceae]
marker32 k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Eubacteriaceae
marker33 k__Bacteria|p__Firmicutes|c__Erysipelotrichi|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Coprobacillus
marker34 k__Bacteria|p__Firmicutes|c__Erysipelotrichi|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Coprobacillus|g__Coprobacillus_s__
enrich_group ef_logFC pvalue padj
marker1 CD -4.7938 1.7225e-06 0.00080748
marker2 CD -5.2183 3.0820e-06 0.00080748
marker3 CD -5.2183 3.0820e-06 0.00080748
marker4 CD -9.5469 5.7230e-06 0.00089966
marker5 CD -9.5469 5.7230e-06 0.00089966
marker6 CD -5.2156 9.1574e-06 0.00102824
marker7 CD -5.2156 9.1574e-06 0.00102824
marker8 Control 8.0864 2.0042e-05 0.00196912
marker9 Control 9.0024 2.9510e-05 0.00226870
marker10 Control 9.0024 2.9510e-05 0.00226870
marker11 CD -3.4448 3.1750e-05 0.00226870
marker12 Control 3.2158 1.3357e-04 0.00874873
marker13 Control 3.1378 2.0167e-04 0.01219313
marker14 Control 5.0967 2.6625e-04 0.01457664
marker15 Control 8.3773 3.7962e-04 0.01457664
marker16 Control 8.3773 3.7962e-04 0.01457664
marker17 Control 8.3773 3.7962e-04 0.01457664
marker18 Control 8.3773 3.7962e-04 0.01457664
marker19 Control 8.3773 3.7962e-04 0.01457664
marker20 CD -3.7258 4.0771e-04 0.01457664
marker21 CD -3.7256 4.0800e-04 0.01457664
marker22 CD -3.7256 4.0800e-04 0.01457664
marker23 CD -3.6959 4.4733e-04 0.01528713
marker24 CD -6.5872 5.8173e-04 0.01879493
marker25 CD -3.4967 5.9780e-04 0.01879493
marker26 Control 3.0131 9.5040e-04 0.02766728
marker27 Control 3.0131 9.5040e-04 0.02766728
marker28 CD -3.7715 1.1025e-03 0.03042827
marker29 Control 3.0180 1.1227e-03 0.03042827
marker30 CD -8.2442 2.1199e-03 0.05554251
marker31 Control 6.5572 2.8503e-03 0.07226790
marker32 Control 5.4734 3.7850e-03 0.08918605
marker33 Control 5.4044 3.8579e-03 0.08918605
marker34 Control 5.4044 3.8579e-03 0.08918605
yiluheihei/microbiomeMarker documentation built on Nov. 5, 2023, 7:19 a.m.
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result of edger
Code
print(marker_table(mm_edger), digits = 5)
Output
feature
marker1 k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria
marker2 k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales
marker3 k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales|f__Enterobacteriaceae
marker4 k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales|f__Enterobacteriaceae|g__Klebsiella
marker5 k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales|f__Enterobacteriaceae|g__Klebsiella|g__Klebsiella_s__
marker6 k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales|f__Enterobacteriaceae|g__Escherichia
marker7 k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales|f__Enterobacteriaceae|g__Escherichia|s__coli
marker8 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__adolescentis
marker9 k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__[Paraprevotellaceae]|g__Paraprevotella
marker10 k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__[Paraprevotellaceae]|g__Paraprevotella|g__Paraprevotella_s__
marker11 k__Bacteria|p__Proteobacteria
marker12 k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Roseburia
marker13 k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Roseburia|g__Roseburia_s__
marker14 k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Clostridiaceae|f__Clostridiaceae_g__Clostridium|f__Clostridiaceae_g__Clostridium_s__
marker15 k__Bacteria|p__Cyanobacteria|c__4C0d-2
marker16 k__Bacteria|p__Cyanobacteria|c__4C0d-2|o__YS2
marker17 k__Bacteria|p__Cyanobacteria|c__4C0d-2|o__YS2|o__YS2_f__
marker18 k__Bacteria|p__Cyanobacteria|c__4C0d-2|o__YS2|o__YS2_f__|o__YS2_f___g__
marker19 k__Bacteria|p__Cyanobacteria|c__4C0d-2|o__YS2|o__YS2_f__|o__YS2_f___g__|o__YS2_f___g___s__
marker20 k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rickettsiales|f__mitochondria
marker21 k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rickettsiales|f__mitochondria|f__mitochondria_g__
marker22 k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rickettsiales|f__mitochondria|f__mitochondria_g__|f__mitochondria_g___s__
marker23 k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rickettsiales
marker24 k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|g__Prevotella_s__
marker25 k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria
marker26 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Bifidobacteriales
marker27 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Bifidobacteriales|f__Bifidobacteriaceae
marker28 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Actinomycetales
marker29 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium
marker30 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Actinomycetales|f__Nocardioidaceae
marker31 k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__[Paraprevotellaceae]
marker32 k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Eubacteriaceae
marker33 k__Bacteria|p__Firmicutes|c__Erysipelotrichi|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Coprobacillus
marker34 k__Bacteria|p__Firmicutes|c__Erysipelotrichi|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Coprobacillus|g__Coprobacillus_s__
enrich_group ef_logFC pvalue padj
marker1 CD -4.7938 1.7225e-06 0.00080748
marker2 CD -5.2183 3.0820e-06 0.00080748
marker3 CD -5.2183 3.0820e-06 0.00080748
marker4 CD -9.5469 5.7230e-06 0.00089966
marker5 CD -9.5469 5.7230e-06 0.00089966
marker6 CD -5.2156 9.1574e-06 0.00102824
marker7 CD -5.2156 9.1574e-06 0.00102824
marker8 Control 8.0864 2.0042e-05 0.00196912
marker9 Control 9.0024 2.9510e-05 0.00226870
marker10 Control 9.0024 2.9510e-05 0.00226870
marker11 CD -3.4448 3.1750e-05 0.00226870
marker12 Control 3.2158 1.3357e-04 0.00874873
marker13 Control 3.1378 2.0167e-04 0.01219313
marker14 Control 5.0967 2.6625e-04 0.01457664
marker15 Control 8.3773 3.7962e-04 0.01457664
marker16 Control 8.3773 3.7962e-04 0.01457664
marker17 Control 8.3773 3.7962e-04 0.01457664
marker18 Control 8.3773 3.7962e-04 0.01457664
marker19 Control 8.3773 3.7962e-04 0.01457664
marker20 CD -3.7258 4.0771e-04 0.01457664
marker21 CD -3.7256 4.0800e-04 0.01457664
marker22 CD -3.7256 4.0800e-04 0.01457664
marker23 CD -3.6959 4.4733e-04 0.01528713
marker24 CD -6.5872 5.8173e-04 0.01879493
marker25 CD -3.4967 5.9780e-04 0.01879493
marker26 Control 3.0131 9.5040e-04 0.02766728
marker27 Control 3.0131 9.5040e-04 0.02766728
marker28 CD -3.7715 1.1025e-03 0.03042827
marker29 Control 3.0180 1.1227e-03 0.03042827
marker30 CD -8.2442 2.1199e-03 0.05554251
marker31 Control 6.5572 2.8503e-03 0.07226790
marker32 Control 5.4734 3.7850e-03 0.08918605
marker33 Control 5.4044 3.8579e-03 0.08918605
marker34 Control 5.4044 3.8579e-03 0.08918605
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