BIOMannotations: Search and change row or column annotations of BIOM data
In matR: Metagenomics Analysis Tools
Description
Usage
Arguments
Details
Value
Author(s)
See Also
Examples
Description
For an object of class biom,
find row or column annotations (BIOM metadata)
that match by name a given pattern,
or append new annotations.
Usage
1
2
3
4
5
Arguments
x
an object (biom)
pattern
literal string or regular expression identifying metadata by name (character)
name
name for new metadata annotation (character)
value
new metadata, one value per row/column
Details
Complete technical documentation is forthcoming.
For the current preliminary release, please refer
to the examples provided.
Value
For rows() and columns(),
a data.frame consisting of the metadata of x matching pattern by name.
For the replacement functions,
the object x with updated metadata.
Author(s)
Daniel T. Braithwaite
See Also
Examples
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
#### exact sampling locations returned in a data.frame
columns (xx3, "latitude|longitude")
#### a data.frame is returned even in case of a single matching metadata field
is.data.frame (columns (xx1, "sample.data.biome"))
#### project IDs and environmental package metadata -- note regex here and above
colnames (columns (xx2, "project\\.id|^env_package"))
#### row metadata makes annotation hierarchy levels available,
#### so typical row metadata has few components, and here just two
names (rows (xx1))
rows (xx1, "ontology1")
#### here, the rownames and the (single) variable of the data.frame coincide
rows (xx1, "ontology2")
#### variables are almost always coded as factors
is.factor (columns (xx1, "sample.data.biome") [[1]])
Example output
Loading required package: MGRASTer
MGRASTer (0.9 02e288)
Loading required package: BIOM.utils
BIOM.utils (0.9 dbcb27)
matR: metagenomics analysis tools for R (0.9.1)
sample.data.latitude sample.data.longitude
mgm4477803.3 -77.725 162.311
mgm4477804.3 39.1 -96.6
mgm4477805.3 34.9 -115.65
mgm4477807.3 -12.633 -71.233
mgm4477872.3 35.383 -105.933
mgm4477873.3 34.333 -106.733
mgm4477874.3 68.633 -149.583
mgm4477875.3 -26.733 -54.683
mgm4477876.3 64.8 -148.25
mgm4477877.3 34.617 -81.667
mgm4477899.3 35.967 -79.083
mgm4477900.3 -78.03 163.873283333333
mgm4477901.3 -77.725 162.313
mgm4477902.3 -77.608 163.249
mgm4477903.3 -77.6375 162.887
mgm4477904.3 -77.527 161.702
mgm4575382.3 -26.733 -54.683
mgm4575383.3 64.8 -148.25
mgm4575384.3 34.617 -81.667
mgm4575385.3 35.967 -79.083
mgm4575386.3 -78.03 163.873283333333
mgm4575387.3 -77.725 162.313
mgm4575388.3 -77.608 163.249
mgm4575389.3 -77.6375 162.887
mgm4575390.3 -77.527 161.702
mgm4575391.3 -77.725 162.311
mgm4575392.3 39.1 -96.6
mgm4575393.3 34.9 -115.65
mgm4575394.3 -12.633 -71.233
mgm4575395.3 35.383 -105.933
mgm4575396.3 34.333 -106.733
mgm4575397.3 68.633 -149.583
[1] TRUE
[1] "env_package.data.alkalinity"
[2] "env_package.data.ammonium"
[3] "env_package.data.bromide"
[4] "env_package.data.calcium"
[5] "env_package.data.chloride"
[6] "env_package.data.density"
[7] "env_package.data.diss_org_carb"
[8] "env_package.data.env_package"
[9] "env_package.data.magnesium"
[10] "env_package.data.misc_param"
[11] "env_package.data.nitrate"
[12] "env_package.data.nitrite"
[13] "env_package.data.potassium"
[14] "env_package.data.salinity"
[15] "env_package.data.samp_store_temp"
[16] "env_package.data.silicate"
[17] "env_package.data.sulfate"
[18] "env_package.data.suspend_part_matter"
[19] "env_package.id"
[20] "env_package.name"
[21] "env_package.type"
[22] "project.id"
[1] "ontology1" "ontology2"
ontology1
ABC transporters Membrane Transport
ATP synthases Respiration
Acid stress Stress Response
Adhesion Virulence, Disease and Defense
Alanine, serine, and glycine Amino Acids and Derivatives
Aminosugars Carbohydrates
Anaerobic degradation of aromatic compounds Metabolism of Aromatic Compounds
Arginine; urea cycle, polyamines Amino Acids and Derivatives
Aromatic amino acids and derivatives Amino Acids and Derivatives
Bacterial cytostatics, differentiation factors and antibiotics Secondary Metabolism
Bacteriocins, ribosomally synthesized antibacterial peptides Virulence, Disease and Defense
Biologically active compounds in metazoan cell defence and differentiation Secondary Metabolism
Biosynthesis of galactoglycans and related lipopolysacharides Clustering-based subsystems
Biosynthesis of phenylpropanoids Secondary Metabolism
Biotin Cofactors, Vitamins, Prosthetic Groups, Pigments
Branched-chain amino acids Amino Acids and Derivatives
CO2 fixation Carbohydrates
CRISPRs and associated hypotheticals Clustering-based subsystems
CRISPs DNA Metabolism
Capsular and extracellular polysacchrides Cell Wall and Capsule
Carbohydrates Clustering-based subsystems
Carotenoid biosynthesis Clustering-based subsystems
Cell Division Clustering-based subsystems
Cell wall of Mycobacteria Cell Wall and Capsule
Central carbohydrate metabolism Carbohydrates
Chemotaxis, response regulators Clustering-based subsystems
Choline bitartrate degradation, putative Clustering-based subsystems
Chromosome Replication Clustering-based subsystems
Clustering-based subsystems Clustering-based subsystems
Coenzyme A Cofactors, Vitamins, Prosthetic Groups, Pigments
Coenzyme B Cofactors, Vitamins, Prosthetic Groups, Pigments
Coenzyme F420 Cofactors, Vitamins, Prosthetic Groups, Pigments
Coenzyme M Cofactors, Vitamins, Prosthetic Groups, Pigments
Cold shock Stress Response
Cytochrome biogenesis Clustering-based subsystems
D-tyrosyl-tRNA(Tyr) deacylase (EC 3.1.-.-) cluster Clustering-based subsystems
DNA metabolism Clustering-based subsystems
DNA polymerase III epsilon cluster Clustering-based subsystems
DNA recombination DNA Metabolism
DNA repair DNA Metabolism
DNA replication DNA Metabolism
DNA uptake, competence DNA Metabolism
Detection Virulence, Disease and Defense
Detoxification Nucleosides and Nucleotides
Di- and oligosaccharides Carbohydrates
Electron accepting reactions Respiration
Electron donating reactions Respiration
Electron transport and photophosphorylation Photosynthesis
Fatty acid metabolic cluster Clustering-based subsystems
Fatty acids Fatty Acids, Lipids, and Isoprenoids
Fermentation Carbohydrates
Flagella protein? Clustering-based subsystems
Flagellar motility in Prokaryota Motility and Chemotaxis
Folate and pterines Cofactors, Vitamins, Prosthetic Groups, Pigments
Gene Transfer Agent (GTA) Phages, Prophages, Transposable elements, Plasmids
Glutamine, glutamate, aspartate, asparagine; ammonia assimilation Amino Acids and Derivatives
Glycoside hydrolases Carbohydrates
Gram-Negative cell wall components Cell Wall and Capsule
Gram-Positive cell wall components Cell Wall and Capsule
Heat shock Stress Response
Histidine Metabolism Amino Acids and Derivatives
Hypothetical Related to Dihydroorate Dehydrogenase Clustering-based subsystems
Hypothetical associated with RecF Clustering-based subsystems
Hypothetical in Lysine biosynthetic cluster Clustering-based subsystems
Hypothetical lipase related to Phosphatidate metabolism Clustering-based subsystems
Hypothetical protein possible functionally linked with Alanyl-tRNA synthetase Clustering-based subsystems
Inorganic sulfur assimilation Sulfur Metabolism
Invasion and intracellular resistance Virulence, Disease and Defense
Isoprenoid/cell wall biosynthesis: PREDICTED UNDECAPRENYL DIPHOSPHATE PHOSPHATASE Clustering-based subsystems
Isoprenoids Fatty Acids, Lipids, and Isoprenoids
Lipid-derived mediators Secondary Metabolism
Lipoic acid Cofactors, Vitamins, Prosthetic Groups, Pigments
Lysine Biosynthesis Clustering-based subsystems
Lysine, threonine, methionine, and cysteine Amino Acids and Derivatives
Metabolism of central aromatic intermediates Metabolism of Aromatic Compounds
Methylamine utilization Clustering-based subsystems
Molybdopterin oxidoreductase Clustering-based subsystems
Monosaccharides Clustering-based subsystems
NAD and NADP Cofactors, Vitamins, Prosthetic Groups, Pigments
Nucleotidyl-phosphate metabolic cluster Clustering-based subsystems
One-carbon Metabolism Carbohydrates
Organic acids Carbohydrates
Organic sulfur assimilation Sulfur Metabolism
Osmotic stress Stress Response
Oxidative stress Stress Response
Pathogenicity islands Phages, Prophages, Transposable elements, Plasmids
Peripheral pathways for catabolism of aromatic compounds Metabolism of Aromatic Compounds
Periplasmic Stress Stress Response
Phages, Prophages Phages, Prophages, Transposable elements, Plasmids
Phosphate metabolism Clustering-based subsystems
Phospholipids Fatty Acids, Lipids, and Isoprenoids
Plant Alkaloids Secondary Metabolism
Plant Hormones Secondary Metabolism
Plant-Prokaryote DOE project Miscellaneous
Plasmid related functions Phages, Prophages, Transposable elements, Plasmids
Polysaccharides Carbohydrates
Probably GTP or GMP signaling related Clustering-based subsystems
Probably Pyrimidine biosynthesis-related Clustering-based subsystems
Probably Ybbk-related hypothetical membrane proteins Clustering-based subsystems
Probably organic hydroperoxide resistance related hypothetical protein Clustering-based subsystems
Programmed Cell Death and Toxin-antitoxin Systems Regulation and Cell signaling
Proline and 4-hydroxyproline Amino Acids and Derivatives
Proteasome related clusters Clustering-based subsystems
Protein and nucleoprotein secretion system, Type IV Membrane Transport
Protein biosynthesis Protein Metabolism
Protein degradation Protein Metabolism
Protein export? Clustering-based subsystems
Protein folding Protein Metabolism
Protein processing and modification Protein Metabolism
Protein secretion system, Type I Membrane Transport
Protein secretion system, Type II Membrane Transport
Protein secretion system, Type III Membrane Transport
Protein secretion system, Type V Membrane Transport
Protein secretion system, Type VI Membrane Transport
Protein secretion system, Type VII (Chaperone/Usher pathway, CU) Membrane Transport
Protein secretion system, Type VIII (Extracellular nucleation/precipitation pathway, ENP) Membrane Transport
Protein translocation across cytoplasmic membrane Membrane Transport
Proteolytic pathway Regulation and Cell signaling
Purines Nucleosides and Nucleotides
Putative GGDEF domain protein related to agglutinin secretion Clustering-based subsystems
Putative Isoquinoline 1-oxidoreductase subunit Clustering-based subsystems
Putative asociate of RNA polymerase sigma-54 factor rpoN Clustering-based subsystems
Putrescine/GABA utilization cluster-temporal,to add to SSs Clustering-based subsystems
Pyridoxine Cofactors, Vitamins, Prosthetic Groups, Pigments
Pyrimidines Nucleosides and Nucleotides
Pyruvate kinase associated cluster Clustering-based subsystems
Quinone cofactors Cofactors, Vitamins, Prosthetic Groups, Pigments
Quorum sensing and biofilm formation Regulation and Cell signaling
RNA processing and modification RNA Metabolism
Recombination related cluster Clustering-based subsystems
Regulation of virulence Regulation and Cell signaling
Related to Menaquinone-cytochrome C reductase Clustering-based subsystems
Resistance to antibiotics and toxic compounds Virulence, Disease and Defense
Reverse electron transport Respiration
Riboflavin, FMN, FAD Cofactors, Vitamins, Prosthetic Groups, Pigments
Ribosomal Protein L28P relates to a set of uncharacterized proteins Clustering-based subsystems
Ribosome-related cluster Clustering-based subsystems
Sarcosine oxidase Clustering-based subsystems
Selenoproteins Protein Metabolism
Shiga toxin cluster Clustering-based subsystems
Siderophores Iron acquisition and metabolism
Sodium Ion-Coupled Energetics Respiration
Spore DNA protection Dormancy and Sporulation
Sugar Phosphotransferase Systems, PTS Membrane Transport
Sugar alcohols Carbohydrates
Sulfatases and sulfatase modifying factor 1 (and a hypothetical) Clustering-based subsystems
Tetrapyrroles Cofactors, Vitamins, Prosthetic Groups, Pigments
Three hypotheticals linked to lipoprotein biosynthesis Clustering-based subsystems
TldD cluster Clustering-based subsystems
Toxins and superantigens Virulence, Disease and Defense
Transcription RNA Metabolism
Translation Clustering-based subsystems
Transposable elements Phages, Prophages, Transposable elements, Plasmids
Triacylglycerols Fatty Acids, Lipids, and Isoprenoids
Tricarboxylate transporter Clustering-based subsystems
Two related proteases Clustering-based subsystems
Uni- Sym- and Antiporters Membrane Transport
alpha-proteobacterial cluster of hypotheticals Clustering-based subsystems
proteosome related Clustering-based subsystems
recX and regulatory cluster Clustering-based subsystems
tRNA sulfuration Clustering-based subsystems
ontology2
ABC transporters ABC transporters
ATP synthases ATP synthases
Acid stress Acid stress
Adhesion Adhesion
Alanine, serine, and glycine Alanine, serine, and glycine
Aminosugars Aminosugars
Anaerobic degradation of aromatic compounds Anaerobic degradation of aromatic compounds
Arginine; urea cycle, polyamines Arginine; urea cycle, polyamines
Aromatic amino acids and derivatives Aromatic amino acids and derivatives
Bacterial cytostatics, differentiation factors and antibiotics Bacterial cytostatics, differentiation factors and antibiotics
Bacteriocins, ribosomally synthesized antibacterial peptides Bacteriocins, ribosomally synthesized antibacterial peptides
Biologically active compounds in metazoan cell defence and differentiation Biologically active compounds in metazoan cell defence and differentiation
Biosynthesis of galactoglycans and related lipopolysacharides Biosynthesis of galactoglycans and related lipopolysacharides
Biosynthesis of phenylpropanoids Biosynthesis of phenylpropanoids
Biotin Biotin
Branched-chain amino acids Branched-chain amino acids
CO2 fixation CO2 fixation
CRISPRs and associated hypotheticals CRISPRs and associated hypotheticals
CRISPs CRISPs
Capsular and extracellular polysacchrides Capsular and extracellular polysacchrides
Carbohydrates Carbohydrates
Carotenoid biosynthesis Carotenoid biosynthesis
Cell Division Cell Division
Cell wall of Mycobacteria Cell wall of Mycobacteria
Central carbohydrate metabolism Central carbohydrate metabolism
Chemotaxis, response regulators Chemotaxis, response regulators
Choline bitartrate degradation, putative Choline bitartrate degradation, putative
Chromosome Replication Chromosome Replication
Clustering-based subsystems Clustering-based subsystems
Coenzyme A Coenzyme A
Coenzyme B Coenzyme B
Coenzyme F420 Coenzyme F420
Coenzyme M Coenzyme M
Cold shock Cold shock
Cytochrome biogenesis Cytochrome biogenesis
D-tyrosyl-tRNA(Tyr) deacylase (EC 3.1.-.-) cluster D-tyrosyl-tRNA(Tyr) deacylase (EC 3.1.-.-) cluster
DNA metabolism DNA metabolism
DNA polymerase III epsilon cluster DNA polymerase III epsilon cluster
DNA recombination DNA recombination
DNA repair DNA repair
DNA replication DNA replication
DNA uptake, competence DNA uptake, competence
Detection Detection
Detoxification Detoxification
Di- and oligosaccharides Di- and oligosaccharides
Electron accepting reactions Electron accepting reactions
Electron donating reactions Electron donating reactions
Electron transport and photophosphorylation Electron transport and photophosphorylation
Fatty acid metabolic cluster Fatty acid metabolic cluster
Fatty acids Fatty acids
Fermentation Fermentation
Flagella protein? Flagella protein?
Flagellar motility in Prokaryota Flagellar motility in Prokaryota
Folate and pterines Folate and pterines
Gene Transfer Agent (GTA) Gene Transfer Agent (GTA)
Glutamine, glutamate, aspartate, asparagine; ammonia assimilation Glutamine, glutamate, aspartate, asparagine; ammonia assimilation
Glycoside hydrolases Glycoside hydrolases
Gram-Negative cell wall components Gram-Negative cell wall components
Gram-Positive cell wall components Gram-Positive cell wall components
Heat shock Heat shock
Histidine Metabolism Histidine Metabolism
Hypothetical Related to Dihydroorate Dehydrogenase Hypothetical Related to Dihydroorate Dehydrogenase
Hypothetical associated with RecF Hypothetical associated with RecF
Hypothetical in Lysine biosynthetic cluster Hypothetical in Lysine biosynthetic cluster
Hypothetical lipase related to Phosphatidate metabolism Hypothetical lipase related to Phosphatidate metabolism
Hypothetical protein possible functionally linked with Alanyl-tRNA synthetase Hypothetical protein possible functionally linked with Alanyl-tRNA synthetase
Inorganic sulfur assimilation Inorganic sulfur assimilation
Invasion and intracellular resistance Invasion and intracellular resistance
Isoprenoid/cell wall biosynthesis: PREDICTED UNDECAPRENYL DIPHOSPHATE PHOSPHATASE Isoprenoid/cell wall biosynthesis: PREDICTED UNDECAPRENYL DIPHOSPHATE PHOSPHATASE
Isoprenoids Isoprenoids
Lipid-derived mediators Lipid-derived mediators
Lipoic acid Lipoic acid
Lysine Biosynthesis Lysine Biosynthesis
Lysine, threonine, methionine, and cysteine Lysine, threonine, methionine, and cysteine
Metabolism of central aromatic intermediates Metabolism of central aromatic intermediates
Methylamine utilization Methylamine utilization
Molybdopterin oxidoreductase Molybdopterin oxidoreductase
Monosaccharides Monosaccharides
NAD and NADP NAD and NADP
Nucleotidyl-phosphate metabolic cluster Nucleotidyl-phosphate metabolic cluster
One-carbon Metabolism One-carbon Metabolism
Organic acids Organic acids
Organic sulfur assimilation Organic sulfur assimilation
Osmotic stress Osmotic stress
Oxidative stress Oxidative stress
Pathogenicity islands Pathogenicity islands
Peripheral pathways for catabolism of aromatic compounds Peripheral pathways for catabolism of aromatic compounds
Periplasmic Stress Periplasmic Stress
Phages, Prophages Phages, Prophages
Phosphate metabolism Phosphate metabolism
Phospholipids Phospholipids
Plant Alkaloids Plant Alkaloids
Plant Hormones Plant Hormones
Plant-Prokaryote DOE project Plant-Prokaryote DOE project
Plasmid related functions Plasmid related functions
Polysaccharides Polysaccharides
Probably GTP or GMP signaling related Probably GTP or GMP signaling related
Probably Pyrimidine biosynthesis-related Probably Pyrimidine biosynthesis-related
Probably Ybbk-related hypothetical membrane proteins Probably Ybbk-related hypothetical membrane proteins
Probably organic hydroperoxide resistance related hypothetical protein Probably organic hydroperoxide resistance related hypothetical protein
Programmed Cell Death and Toxin-antitoxin Systems Programmed Cell Death and Toxin-antitoxin Systems
Proline and 4-hydroxyproline Proline and 4-hydroxyproline
Proteasome related clusters Proteasome related clusters
Protein and nucleoprotein secretion system, Type IV Protein and nucleoprotein secretion system, Type IV
Protein biosynthesis Protein biosynthesis
Protein degradation Protein degradation
Protein export? Protein export?
Protein folding Protein folding
Protein processing and modification Protein processing and modification
Protein secretion system, Type I Protein secretion system, Type I
Protein secretion system, Type II Protein secretion system, Type II
Protein secretion system, Type III Protein secretion system, Type III
Protein secretion system, Type V Protein secretion system, Type V
Protein secretion system, Type VI Protein secretion system, Type VI
Protein secretion system, Type VII (Chaperone/Usher pathway, CU) Protein secretion system, Type VII (Chaperone/Usher pathway, CU)
Protein secretion system, Type VIII (Extracellular nucleation/precipitation pathway, ENP) Protein secretion system, Type VIII (Extracellular nucleation/precipitation pathway, ENP)
Protein translocation across cytoplasmic membrane Protein translocation across cytoplasmic membrane
Proteolytic pathway Proteolytic pathway
Purines Purines
Putative GGDEF domain protein related to agglutinin secretion Putative GGDEF domain protein related to agglutinin secretion
Putative Isoquinoline 1-oxidoreductase subunit Putative Isoquinoline 1-oxidoreductase subunit
Putative asociate of RNA polymerase sigma-54 factor rpoN Putative asociate of RNA polymerase sigma-54 factor rpoN
Putrescine/GABA utilization cluster-temporal,to add to SSs Putrescine/GABA utilization cluster-temporal,to add to SSs
Pyridoxine Pyridoxine
Pyrimidines Pyrimidines
Pyruvate kinase associated cluster Pyruvate kinase associated cluster
Quinone cofactors Quinone cofactors
Quorum sensing and biofilm formation Quorum sensing and biofilm formation
RNA processing and modification RNA processing and modification
Recombination related cluster Recombination related cluster
Regulation of virulence Regulation of virulence
Related to Menaquinone-cytochrome C reductase Related to Menaquinone-cytochrome C reductase
Resistance to antibiotics and toxic compounds Resistance to antibiotics and toxic compounds
Reverse electron transport Reverse electron transport
Riboflavin, FMN, FAD Riboflavin, FMN, FAD
Ribosomal Protein L28P relates to a set of uncharacterized proteins Ribosomal Protein L28P relates to a set of uncharacterized proteins
Ribosome-related cluster Ribosome-related cluster
Sarcosine oxidase Sarcosine oxidase
Selenoproteins Selenoproteins
Shiga toxin cluster Shiga toxin cluster
Siderophores Siderophores
Sodium Ion-Coupled Energetics Sodium Ion-Coupled Energetics
Spore DNA protection Spore DNA protection
Sugar Phosphotransferase Systems, PTS Sugar Phosphotransferase Systems, PTS
Sugar alcohols Sugar alcohols
Sulfatases and sulfatase modifying factor 1 (and a hypothetical) Sulfatases and sulfatase modifying factor 1 (and a hypothetical)
Tetrapyrroles Tetrapyrroles
Three hypotheticals linked to lipoprotein biosynthesis Three hypotheticals linked to lipoprotein biosynthesis
TldD cluster TldD cluster
Toxins and superantigens Toxins and superantigens
Transcription Transcription
Translation Translation
Transposable elements Transposable elements
Triacylglycerols Triacylglycerols
Tricarboxylate transporter Tricarboxylate transporter
Two related proteases Two related proteases
Uni- Sym- and Antiporters Uni- Sym- and Antiporters
alpha-proteobacterial cluster of hypotheticals alpha-proteobacterial cluster of hypotheticals
proteosome related proteosome related
recX and regulatory cluster recX and regulatory cluster
tRNA sulfuration tRNA sulfuration
[1] TRUE
matR documentation built on May 2, 2019, 6:53 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description Usage Arguments Details Value Author(s) See Also Examples
Description
For an object of class biom,
find row or column annotations (BIOM metadata)
that match by name a given pattern,
or append new annotations.
Usage
1 2 3 4 5 |
Arguments
x |
an object ( |
pattern |
literal string or regular expression identifying metadata by name ( |
name |
name for new metadata annotation ( |
value |
new metadata, one value per row/column |
Details
Complete technical documentation is forthcoming. For the current preliminary release, please refer to the examples provided.
Value
For rows() and columns(),
a data.frame consisting of the metadata of x matching pattern by name.
For the replacement functions,
the object x with updated metadata.
Author(s)
Daniel T. Braithwaite
See Also
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 | #### exact sampling locations returned in a data.frame
columns (xx3, "latitude|longitude")
#### a data.frame is returned even in case of a single matching metadata field
is.data.frame (columns (xx1, "sample.data.biome"))
#### project IDs and environmental package metadata -- note regex here and above
colnames (columns (xx2, "project\\.id|^env_package"))
#### row metadata makes annotation hierarchy levels available,
#### so typical row metadata has few components, and here just two
names (rows (xx1))
rows (xx1, "ontology1")
#### here, the rownames and the (single) variable of the data.frame coincide
rows (xx1, "ontology2")
#### variables are almost always coded as factors
is.factor (columns (xx1, "sample.data.biome") [[1]])
|
Example output
Loading required package: MGRASTer
MGRASTer (0.9 02e288)
Loading required package: BIOM.utils
BIOM.utils (0.9 dbcb27)
matR: metagenomics analysis tools for R (0.9.1)
sample.data.latitude sample.data.longitude
mgm4477803.3 -77.725 162.311
mgm4477804.3 39.1 -96.6
mgm4477805.3 34.9 -115.65
mgm4477807.3 -12.633 -71.233
mgm4477872.3 35.383 -105.933
mgm4477873.3 34.333 -106.733
mgm4477874.3 68.633 -149.583
mgm4477875.3 -26.733 -54.683
mgm4477876.3 64.8 -148.25
mgm4477877.3 34.617 -81.667
mgm4477899.3 35.967 -79.083
mgm4477900.3 -78.03 163.873283333333
mgm4477901.3 -77.725 162.313
mgm4477902.3 -77.608 163.249
mgm4477903.3 -77.6375 162.887
mgm4477904.3 -77.527 161.702
mgm4575382.3 -26.733 -54.683
mgm4575383.3 64.8 -148.25
mgm4575384.3 34.617 -81.667
mgm4575385.3 35.967 -79.083
mgm4575386.3 -78.03 163.873283333333
mgm4575387.3 -77.725 162.313
mgm4575388.3 -77.608 163.249
mgm4575389.3 -77.6375 162.887
mgm4575390.3 -77.527 161.702
mgm4575391.3 -77.725 162.311
mgm4575392.3 39.1 -96.6
mgm4575393.3 34.9 -115.65
mgm4575394.3 -12.633 -71.233
mgm4575395.3 35.383 -105.933
mgm4575396.3 34.333 -106.733
mgm4575397.3 68.633 -149.583
[1] TRUE
[1] "env_package.data.alkalinity"
[2] "env_package.data.ammonium"
[3] "env_package.data.bromide"
[4] "env_package.data.calcium"
[5] "env_package.data.chloride"
[6] "env_package.data.density"
[7] "env_package.data.diss_org_carb"
[8] "env_package.data.env_package"
[9] "env_package.data.magnesium"
[10] "env_package.data.misc_param"
[11] "env_package.data.nitrate"
[12] "env_package.data.nitrite"
[13] "env_package.data.potassium"
[14] "env_package.data.salinity"
[15] "env_package.data.samp_store_temp"
[16] "env_package.data.silicate"
[17] "env_package.data.sulfate"
[18] "env_package.data.suspend_part_matter"
[19] "env_package.id"
[20] "env_package.name"
[21] "env_package.type"
[22] "project.id"
[1] "ontology1" "ontology2"
ontology1
ABC transporters Membrane Transport
ATP synthases Respiration
Acid stress Stress Response
Adhesion Virulence, Disease and Defense
Alanine, serine, and glycine Amino Acids and Derivatives
Aminosugars Carbohydrates
Anaerobic degradation of aromatic compounds Metabolism of Aromatic Compounds
Arginine; urea cycle, polyamines Amino Acids and Derivatives
Aromatic amino acids and derivatives Amino Acids and Derivatives
Bacterial cytostatics, differentiation factors and antibiotics Secondary Metabolism
Bacteriocins, ribosomally synthesized antibacterial peptides Virulence, Disease and Defense
Biologically active compounds in metazoan cell defence and differentiation Secondary Metabolism
Biosynthesis of galactoglycans and related lipopolysacharides Clustering-based subsystems
Biosynthesis of phenylpropanoids Secondary Metabolism
Biotin Cofactors, Vitamins, Prosthetic Groups, Pigments
Branched-chain amino acids Amino Acids and Derivatives
CO2 fixation Carbohydrates
CRISPRs and associated hypotheticals Clustering-based subsystems
CRISPs DNA Metabolism
Capsular and extracellular polysacchrides Cell Wall and Capsule
Carbohydrates Clustering-based subsystems
Carotenoid biosynthesis Clustering-based subsystems
Cell Division Clustering-based subsystems
Cell wall of Mycobacteria Cell Wall and Capsule
Central carbohydrate metabolism Carbohydrates
Chemotaxis, response regulators Clustering-based subsystems
Choline bitartrate degradation, putative Clustering-based subsystems
Chromosome Replication Clustering-based subsystems
Clustering-based subsystems Clustering-based subsystems
Coenzyme A Cofactors, Vitamins, Prosthetic Groups, Pigments
Coenzyme B Cofactors, Vitamins, Prosthetic Groups, Pigments
Coenzyme F420 Cofactors, Vitamins, Prosthetic Groups, Pigments
Coenzyme M Cofactors, Vitamins, Prosthetic Groups, Pigments
Cold shock Stress Response
Cytochrome biogenesis Clustering-based subsystems
D-tyrosyl-tRNA(Tyr) deacylase (EC 3.1.-.-) cluster Clustering-based subsystems
DNA metabolism Clustering-based subsystems
DNA polymerase III epsilon cluster Clustering-based subsystems
DNA recombination DNA Metabolism
DNA repair DNA Metabolism
DNA replication DNA Metabolism
DNA uptake, competence DNA Metabolism
Detection Virulence, Disease and Defense
Detoxification Nucleosides and Nucleotides
Di- and oligosaccharides Carbohydrates
Electron accepting reactions Respiration
Electron donating reactions Respiration
Electron transport and photophosphorylation Photosynthesis
Fatty acid metabolic cluster Clustering-based subsystems
Fatty acids Fatty Acids, Lipids, and Isoprenoids
Fermentation Carbohydrates
Flagella protein? Clustering-based subsystems
Flagellar motility in Prokaryota Motility and Chemotaxis
Folate and pterines Cofactors, Vitamins, Prosthetic Groups, Pigments
Gene Transfer Agent (GTA) Phages, Prophages, Transposable elements, Plasmids
Glutamine, glutamate, aspartate, asparagine; ammonia assimilation Amino Acids and Derivatives
Glycoside hydrolases Carbohydrates
Gram-Negative cell wall components Cell Wall and Capsule
Gram-Positive cell wall components Cell Wall and Capsule
Heat shock Stress Response
Histidine Metabolism Amino Acids and Derivatives
Hypothetical Related to Dihydroorate Dehydrogenase Clustering-based subsystems
Hypothetical associated with RecF Clustering-based subsystems
Hypothetical in Lysine biosynthetic cluster Clustering-based subsystems
Hypothetical lipase related to Phosphatidate metabolism Clustering-based subsystems
Hypothetical protein possible functionally linked with Alanyl-tRNA synthetase Clustering-based subsystems
Inorganic sulfur assimilation Sulfur Metabolism
Invasion and intracellular resistance Virulence, Disease and Defense
Isoprenoid/cell wall biosynthesis: PREDICTED UNDECAPRENYL DIPHOSPHATE PHOSPHATASE Clustering-based subsystems
Isoprenoids Fatty Acids, Lipids, and Isoprenoids
Lipid-derived mediators Secondary Metabolism
Lipoic acid Cofactors, Vitamins, Prosthetic Groups, Pigments
Lysine Biosynthesis Clustering-based subsystems
Lysine, threonine, methionine, and cysteine Amino Acids and Derivatives
Metabolism of central aromatic intermediates Metabolism of Aromatic Compounds
Methylamine utilization Clustering-based subsystems
Molybdopterin oxidoreductase Clustering-based subsystems
Monosaccharides Clustering-based subsystems
NAD and NADP Cofactors, Vitamins, Prosthetic Groups, Pigments
Nucleotidyl-phosphate metabolic cluster Clustering-based subsystems
One-carbon Metabolism Carbohydrates
Organic acids Carbohydrates
Organic sulfur assimilation Sulfur Metabolism
Osmotic stress Stress Response
Oxidative stress Stress Response
Pathogenicity islands Phages, Prophages, Transposable elements, Plasmids
Peripheral pathways for catabolism of aromatic compounds Metabolism of Aromatic Compounds
Periplasmic Stress Stress Response
Phages, Prophages Phages, Prophages, Transposable elements, Plasmids
Phosphate metabolism Clustering-based subsystems
Phospholipids Fatty Acids, Lipids, and Isoprenoids
Plant Alkaloids Secondary Metabolism
Plant Hormones Secondary Metabolism
Plant-Prokaryote DOE project Miscellaneous
Plasmid related functions Phages, Prophages, Transposable elements, Plasmids
Polysaccharides Carbohydrates
Probably GTP or GMP signaling related Clustering-based subsystems
Probably Pyrimidine biosynthesis-related Clustering-based subsystems
Probably Ybbk-related hypothetical membrane proteins Clustering-based subsystems
Probably organic hydroperoxide resistance related hypothetical protein Clustering-based subsystems
Programmed Cell Death and Toxin-antitoxin Systems Regulation and Cell signaling
Proline and 4-hydroxyproline Amino Acids and Derivatives
Proteasome related clusters Clustering-based subsystems
Protein and nucleoprotein secretion system, Type IV Membrane Transport
Protein biosynthesis Protein Metabolism
Protein degradation Protein Metabolism
Protein export? Clustering-based subsystems
Protein folding Protein Metabolism
Protein processing and modification Protein Metabolism
Protein secretion system, Type I Membrane Transport
Protein secretion system, Type II Membrane Transport
Protein secretion system, Type III Membrane Transport
Protein secretion system, Type V Membrane Transport
Protein secretion system, Type VI Membrane Transport
Protein secretion system, Type VII (Chaperone/Usher pathway, CU) Membrane Transport
Protein secretion system, Type VIII (Extracellular nucleation/precipitation pathway, ENP) Membrane Transport
Protein translocation across cytoplasmic membrane Membrane Transport
Proteolytic pathway Regulation and Cell signaling
Purines Nucleosides and Nucleotides
Putative GGDEF domain protein related to agglutinin secretion Clustering-based subsystems
Putative Isoquinoline 1-oxidoreductase subunit Clustering-based subsystems
Putative asociate of RNA polymerase sigma-54 factor rpoN Clustering-based subsystems
Putrescine/GABA utilization cluster-temporal,to add to SSs Clustering-based subsystems
Pyridoxine Cofactors, Vitamins, Prosthetic Groups, Pigments
Pyrimidines Nucleosides and Nucleotides
Pyruvate kinase associated cluster Clustering-based subsystems
Quinone cofactors Cofactors, Vitamins, Prosthetic Groups, Pigments
Quorum sensing and biofilm formation Regulation and Cell signaling
RNA processing and modification RNA Metabolism
Recombination related cluster Clustering-based subsystems
Regulation of virulence Regulation and Cell signaling
Related to Menaquinone-cytochrome C reductase Clustering-based subsystems
Resistance to antibiotics and toxic compounds Virulence, Disease and Defense
Reverse electron transport Respiration
Riboflavin, FMN, FAD Cofactors, Vitamins, Prosthetic Groups, Pigments
Ribosomal Protein L28P relates to a set of uncharacterized proteins Clustering-based subsystems
Ribosome-related cluster Clustering-based subsystems
Sarcosine oxidase Clustering-based subsystems
Selenoproteins Protein Metabolism
Shiga toxin cluster Clustering-based subsystems
Siderophores Iron acquisition and metabolism
Sodium Ion-Coupled Energetics Respiration
Spore DNA protection Dormancy and Sporulation
Sugar Phosphotransferase Systems, PTS Membrane Transport
Sugar alcohols Carbohydrates
Sulfatases and sulfatase modifying factor 1 (and a hypothetical) Clustering-based subsystems
Tetrapyrroles Cofactors, Vitamins, Prosthetic Groups, Pigments
Three hypotheticals linked to lipoprotein biosynthesis Clustering-based subsystems
TldD cluster Clustering-based subsystems
Toxins and superantigens Virulence, Disease and Defense
Transcription RNA Metabolism
Translation Clustering-based subsystems
Transposable elements Phages, Prophages, Transposable elements, Plasmids
Triacylglycerols Fatty Acids, Lipids, and Isoprenoids
Tricarboxylate transporter Clustering-based subsystems
Two related proteases Clustering-based subsystems
Uni- Sym- and Antiporters Membrane Transport
alpha-proteobacterial cluster of hypotheticals Clustering-based subsystems
proteosome related Clustering-based subsystems
recX and regulatory cluster Clustering-based subsystems
tRNA sulfuration Clustering-based subsystems
ontology2
ABC transporters ABC transporters
ATP synthases ATP synthases
Acid stress Acid stress
Adhesion Adhesion
Alanine, serine, and glycine Alanine, serine, and glycine
Aminosugars Aminosugars
Anaerobic degradation of aromatic compounds Anaerobic degradation of aromatic compounds
Arginine; urea cycle, polyamines Arginine; urea cycle, polyamines
Aromatic amino acids and derivatives Aromatic amino acids and derivatives
Bacterial cytostatics, differentiation factors and antibiotics Bacterial cytostatics, differentiation factors and antibiotics
Bacteriocins, ribosomally synthesized antibacterial peptides Bacteriocins, ribosomally synthesized antibacterial peptides
Biologically active compounds in metazoan cell defence and differentiation Biologically active compounds in metazoan cell defence and differentiation
Biosynthesis of galactoglycans and related lipopolysacharides Biosynthesis of galactoglycans and related lipopolysacharides
Biosynthesis of phenylpropanoids Biosynthesis of phenylpropanoids
Biotin Biotin
Branched-chain amino acids Branched-chain amino acids
CO2 fixation CO2 fixation
CRISPRs and associated hypotheticals CRISPRs and associated hypotheticals
CRISPs CRISPs
Capsular and extracellular polysacchrides Capsular and extracellular polysacchrides
Carbohydrates Carbohydrates
Carotenoid biosynthesis Carotenoid biosynthesis
Cell Division Cell Division
Cell wall of Mycobacteria Cell wall of Mycobacteria
Central carbohydrate metabolism Central carbohydrate metabolism
Chemotaxis, response regulators Chemotaxis, response regulators
Choline bitartrate degradation, putative Choline bitartrate degradation, putative
Chromosome Replication Chromosome Replication
Clustering-based subsystems Clustering-based subsystems
Coenzyme A Coenzyme A
Coenzyme B Coenzyme B
Coenzyme F420 Coenzyme F420
Coenzyme M Coenzyme M
Cold shock Cold shock
Cytochrome biogenesis Cytochrome biogenesis
D-tyrosyl-tRNA(Tyr) deacylase (EC 3.1.-.-) cluster D-tyrosyl-tRNA(Tyr) deacylase (EC 3.1.-.-) cluster
DNA metabolism DNA metabolism
DNA polymerase III epsilon cluster DNA polymerase III epsilon cluster
DNA recombination DNA recombination
DNA repair DNA repair
DNA replication DNA replication
DNA uptake, competence DNA uptake, competence
Detection Detection
Detoxification Detoxification
Di- and oligosaccharides Di- and oligosaccharides
Electron accepting reactions Electron accepting reactions
Electron donating reactions Electron donating reactions
Electron transport and photophosphorylation Electron transport and photophosphorylation
Fatty acid metabolic cluster Fatty acid metabolic cluster
Fatty acids Fatty acids
Fermentation Fermentation
Flagella protein? Flagella protein?
Flagellar motility in Prokaryota Flagellar motility in Prokaryota
Folate and pterines Folate and pterines
Gene Transfer Agent (GTA) Gene Transfer Agent (GTA)
Glutamine, glutamate, aspartate, asparagine; ammonia assimilation Glutamine, glutamate, aspartate, asparagine; ammonia assimilation
Glycoside hydrolases Glycoside hydrolases
Gram-Negative cell wall components Gram-Negative cell wall components
Gram-Positive cell wall components Gram-Positive cell wall components
Heat shock Heat shock
Histidine Metabolism Histidine Metabolism
Hypothetical Related to Dihydroorate Dehydrogenase Hypothetical Related to Dihydroorate Dehydrogenase
Hypothetical associated with RecF Hypothetical associated with RecF
Hypothetical in Lysine biosynthetic cluster Hypothetical in Lysine biosynthetic cluster
Hypothetical lipase related to Phosphatidate metabolism Hypothetical lipase related to Phosphatidate metabolism
Hypothetical protein possible functionally linked with Alanyl-tRNA synthetase Hypothetical protein possible functionally linked with Alanyl-tRNA synthetase
Inorganic sulfur assimilation Inorganic sulfur assimilation
Invasion and intracellular resistance Invasion and intracellular resistance
Isoprenoid/cell wall biosynthesis: PREDICTED UNDECAPRENYL DIPHOSPHATE PHOSPHATASE Isoprenoid/cell wall biosynthesis: PREDICTED UNDECAPRENYL DIPHOSPHATE PHOSPHATASE
Isoprenoids Isoprenoids
Lipid-derived mediators Lipid-derived mediators
Lipoic acid Lipoic acid
Lysine Biosynthesis Lysine Biosynthesis
Lysine, threonine, methionine, and cysteine Lysine, threonine, methionine, and cysteine
Metabolism of central aromatic intermediates Metabolism of central aromatic intermediates
Methylamine utilization Methylamine utilization
Molybdopterin oxidoreductase Molybdopterin oxidoreductase
Monosaccharides Monosaccharides
NAD and NADP NAD and NADP
Nucleotidyl-phosphate metabolic cluster Nucleotidyl-phosphate metabolic cluster
One-carbon Metabolism One-carbon Metabolism
Organic acids Organic acids
Organic sulfur assimilation Organic sulfur assimilation
Osmotic stress Osmotic stress
Oxidative stress Oxidative stress
Pathogenicity islands Pathogenicity islands
Peripheral pathways for catabolism of aromatic compounds Peripheral pathways for catabolism of aromatic compounds
Periplasmic Stress Periplasmic Stress
Phages, Prophages Phages, Prophages
Phosphate metabolism Phosphate metabolism
Phospholipids Phospholipids
Plant Alkaloids Plant Alkaloids
Plant Hormones Plant Hormones
Plant-Prokaryote DOE project Plant-Prokaryote DOE project
Plasmid related functions Plasmid related functions
Polysaccharides Polysaccharides
Probably GTP or GMP signaling related Probably GTP or GMP signaling related
Probably Pyrimidine biosynthesis-related Probably Pyrimidine biosynthesis-related
Probably Ybbk-related hypothetical membrane proteins Probably Ybbk-related hypothetical membrane proteins
Probably organic hydroperoxide resistance related hypothetical protein Probably organic hydroperoxide resistance related hypothetical protein
Programmed Cell Death and Toxin-antitoxin Systems Programmed Cell Death and Toxin-antitoxin Systems
Proline and 4-hydroxyproline Proline and 4-hydroxyproline
Proteasome related clusters Proteasome related clusters
Protein and nucleoprotein secretion system, Type IV Protein and nucleoprotein secretion system, Type IV
Protein biosynthesis Protein biosynthesis
Protein degradation Protein degradation
Protein export? Protein export?
Protein folding Protein folding
Protein processing and modification Protein processing and modification
Protein secretion system, Type I Protein secretion system, Type I
Protein secretion system, Type II Protein secretion system, Type II
Protein secretion system, Type III Protein secretion system, Type III
Protein secretion system, Type V Protein secretion system, Type V
Protein secretion system, Type VI Protein secretion system, Type VI
Protein secretion system, Type VII (Chaperone/Usher pathway, CU) Protein secretion system, Type VII (Chaperone/Usher pathway, CU)
Protein secretion system, Type VIII (Extracellular nucleation/precipitation pathway, ENP) Protein secretion system, Type VIII (Extracellular nucleation/precipitation pathway, ENP)
Protein translocation across cytoplasmic membrane Protein translocation across cytoplasmic membrane
Proteolytic pathway Proteolytic pathway
Purines Purines
Putative GGDEF domain protein related to agglutinin secretion Putative GGDEF domain protein related to agglutinin secretion
Putative Isoquinoline 1-oxidoreductase subunit Putative Isoquinoline 1-oxidoreductase subunit
Putative asociate of RNA polymerase sigma-54 factor rpoN Putative asociate of RNA polymerase sigma-54 factor rpoN
Putrescine/GABA utilization cluster-temporal,to add to SSs Putrescine/GABA utilization cluster-temporal,to add to SSs
Pyridoxine Pyridoxine
Pyrimidines Pyrimidines
Pyruvate kinase associated cluster Pyruvate kinase associated cluster
Quinone cofactors Quinone cofactors
Quorum sensing and biofilm formation Quorum sensing and biofilm formation
RNA processing and modification RNA processing and modification
Recombination related cluster Recombination related cluster
Regulation of virulence Regulation of virulence
Related to Menaquinone-cytochrome C reductase Related to Menaquinone-cytochrome C reductase
Resistance to antibiotics and toxic compounds Resistance to antibiotics and toxic compounds
Reverse electron transport Reverse electron transport
Riboflavin, FMN, FAD Riboflavin, FMN, FAD
Ribosomal Protein L28P relates to a set of uncharacterized proteins Ribosomal Protein L28P relates to a set of uncharacterized proteins
Ribosome-related cluster Ribosome-related cluster
Sarcosine oxidase Sarcosine oxidase
Selenoproteins Selenoproteins
Shiga toxin cluster Shiga toxin cluster
Siderophores Siderophores
Sodium Ion-Coupled Energetics Sodium Ion-Coupled Energetics
Spore DNA protection Spore DNA protection
Sugar Phosphotransferase Systems, PTS Sugar Phosphotransferase Systems, PTS
Sugar alcohols Sugar alcohols
Sulfatases and sulfatase modifying factor 1 (and a hypothetical) Sulfatases and sulfatase modifying factor 1 (and a hypothetical)
Tetrapyrroles Tetrapyrroles
Three hypotheticals linked to lipoprotein biosynthesis Three hypotheticals linked to lipoprotein biosynthesis
TldD cluster TldD cluster
Toxins and superantigens Toxins and superantigens
Transcription Transcription
Translation Translation
Transposable elements Transposable elements
Triacylglycerols Triacylglycerols
Tricarboxylate transporter Tricarboxylate transporter
Two related proteases Two related proteases
Uni- Sym- and Antiporters Uni- Sym- and Antiporters
alpha-proteobacterial cluster of hypotheticals alpha-proteobacterial cluster of hypotheticals
proteosome related proteosome related
recX and regulatory cluster recX and regulatory cluster
tRNA sulfuration tRNA sulfuration
[1] TRUE
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.