Package 'MicrobiomeProfiler'

Functional enrichment analysis for microbiome data

Description

The package implements an shiny application for functional enrichment analysis and visualiztion of microbiome studies.

---

COG enrichment analysis for microbiome data

Description

COG enrichment analysis for microbiome data

Usage

enrichCOG(
  gene,
  dtype = "category",
  pvalueCutoff = 0.05,
  pAdjustMethod = "BH",
  universe,
  minGSSize = 10,
  maxGSSize = 500,
  qvalueCutoff = 0.2
)

Arguments

gene	a vector of COG ids.
dtype	one of "category", "pathway"
pvalueCutoff	adjusted pvalue cutoff on enrichment tests to report.
pAdjustMethod	one of "holm","hochberg","hommel","bonferroni","BH", "BY","fdr","none".
universe	universe background genes. If missing,use the all COGs.
minGSSize	minimal size of genes annotated by KEGG term for testing.
maxGSSize	maximal size of genes annotated for testing.
qvalueCutoff	qvalue cutoff on enrichment tests to report.

Value

A enrichResult instance.

Examples

data(Psoriasis_data)
cog <- enrichCOG(Psoriasis_data,dtype="category")

---

Metabolism enrichment analysis for microbiome data

Description

Metabolism enrichment analysis for microbiome data

Usage

enrichHMDB(
  metabo_list,
  pvalueCutoff = 0.05,
  pAdjustMethod = "BH",
  universe,
  minGSSize = 10,
  maxGSSize = 500,
  qvalueCutoff = 0.2
)

Arguments

metabo_list	a vector of metabolites in HMDB.ID
pvalueCutoff	adjusted pvalue cutoff on enrichment tests to report.
pAdjustMethod	one of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none".
universe	universe background genes. If missing, use HMDB db.
minGSSize	minimal size of genes annotated by KEGG term for testing.
maxGSSize	maximal size of genes annotated for testing.
qvalueCutoff	qvalue cutoff on enrichment tests to report.

Value

A enrichResult instance.

Examples

x1 <- c("HMDB0000001","HMDB0000005","HMDB0000008")
x2 <- enrichHMDB(x1)

---

KO enrichment for microbiome data

Description

KO enrichment for microbiome data

Usage

enrichKO(
  gene,
  pvalueCutoff = 0.05,
  pAdjustMethod = "BH",
  universe,
  minGSSize = 10,
  maxGSSize = 500,
  qvalueCutoff = 0.2
)

Arguments

gene	a vector of K gene id (e.g. K00001) or EC id (e.g. 1.1.1.27).
pvalueCutoff	adjusted pvalue cutoff on enrichment tests to report.
pAdjustMethod	one of "holm","hochberg","hommel","bonferroni","BH", "BY","fdr","none".
universe	universe background genes. If missing, use all K genes.
minGSSize	minimal size of genes annotated by KEGG term for testing.
maxGSSize	maximal size of genes annotated for testing.
qvalueCutoff	qvalue cutoff on enrichment tests to report.

Value

A enrichResult instance.

Examples

data(Rat_data)
  ko <- enrichKO(Rat_data)
  head(ko)

---

Metabolism enrichment analysis for microbiome data

Description

Metabolism enrichment analysis for microbiome data

Usage

enrichMBKEGG(
  metabo_list,
  pvalueCutoff = 0.05,
  pAdjustMethod = "BH",
  universe,
  minGSSize = 10,
  maxGSSize = 500,
  qvalueCutoff = 0.2
)

Arguments

metabo_list	a vector of metabolites in KEGG.ID
pvalueCutoff	adjusted pvalue cutoff on enrichment tests to report.
pAdjustMethod	one of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none".
universe	universe background genes. If missing, use KEGG as default.
minGSSize	minimal size of genes annotated by KEGG term for testing.
maxGSSize	maximal size of genes annotated for testing.
qvalueCutoff	qvalue cutoff on enrichment tests to report.

Value

A enrichResult instance.

Examples

mblist3 <- c("C00019","C00020","C00022")
mb3 <- enrichMBKEGG(mblist3)
head(mb3)

---

Microbe-Disease associations enrichment analysis

Description

Microbe-Disease associations enrichment analysis

Usage

enrichMDA(
  microbe_list,
  pvalueCutoff = 0.05,
  pAdjustMethod = "BH",
  universe,
  minGSSize = 10,
  maxGSSize = 500,
  qvalueCutoff = 0.2
)

Arguments

microbe_list	a vector of microbe ncbi tax ids.
pvalueCutoff	adjusted pvalue cutoff on enrichment tests to report.
pAdjustMethod	one of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none".
universe	universe background genes. If missing, use disbiome as default.
minGSSize	minimal size of genes annotated by KEGG term for testing.
maxGSSize	maximal size of genes annotated for testing.
qvalueCutoff	qvalue cutoff on enrichment tests to report.

Value

A enrichResult instance.

Examples

data(microbiota_taxlist)
mda <- enrichMDA(microbiota_taxlist)
head(mda)

---

Module enrichment for microbiome data

Description

Module enrichment for microbiome data

Usage

enrichModule(
  gene,
  pvalueCutoff = 0.05,
  pAdjustMethod = "BH",
  universe,
  minGSSize = 10,
  maxGSSize = 500,
  qvalueCutoff = 0.2
)

Arguments

gene	a vector of K gene id (e.g. K00001).
pvalueCutoff	adjusted pvalue cutoff on enrichment tests to report.
pAdjustMethod	one of "holm","hochberg","hommel","bonferroni","BH", "BY","fdr","none".
universe	universe background genes. If missing, use all K genes.
minGSSize	minimal size of genes annotated by KEGG term for testing.
maxGSSize	maximal size of genes annotated for testing.
qvalueCutoff	qvalue cutoff on enrichment tests to report.

Value

A enrichResult instance.

Examples

data(Rat_data)
  ko <- enrichModule(Rat_data)
  head(ko)

---

Metabolism enrichment analysis for microbiome data

Description

Metabolism enrichment analysis for microbiome data

Usage

enrichSMPDB(
  metabo_list,
  pvalueCutoff = 0.05,
  pAdjustMethod = "BH",
  universe,
  minGSSize = 10,
  maxGSSize = 500,
  qvalueCutoff = 0.2
)

Arguments

metabo_list	a vector of metabolites in smpdb Metabolite.ID
pvalueCutoff	adjusted pvalue cutoff on enrichment tests to report.
pAdjustMethod	one of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none".
universe	universe background genes. If missing, use SMPDB db.
minGSSize	minimal size of genes annotated by KEGG term for testing.
maxGSSize	maximal size of genes annotated for testing.
qvalueCutoff	qvalue cutoff on enrichment tests to report.

Value

A enrichResult instance.

Examples

smp <- enrichSMPDB(c("PW_C000164","PW_C000078","PW_C000040"))
head(smp)

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gson_cpd

Description

download compound annotation of the latest version of KEGG pathway and stored in a 'GSON' object

Usage

gson_cpd()

Value

a 'GSON' object

---

gson_enzyme

Description

download compound annotation of the latest version of KEGG pathway to enzyme and stored in a 'GSON' object

Usage

gson_enzyme()

Value

a 'GSON' object

---

gson_KO

Description

download KO annotation of the latest version of KEGG pathway and stored in a 'GSON' object

Usage

gson_KO()

Value

a 'GSON' object

---

gson_module

Description

download compound annotation of the latest version of KEGG Module and stored in a 'GSON' object

Usage

gson_module(db = "ko")

Arguments

db	ko or enzyme

Value

a 'GSON' object

---

Example data: a vector of 54 bacterial genera tested for significantly between T2D metformin samples

Description

This example data was reported on Forslund K,et al.2016 (doi: 10.1038/nature15766) and used for Microbe-Disease Association analysis.

Format

a vector with 54 genera tax ids

References

https://www.nature.com/articles/nature15766

Examples

data(microbiota_taxlist)

---

Example data: a vector of 134 significantly different functional COGs between Psoriasis patients and controls

Description

This example data was reported on Xiao S,et al.2021 (doi:10.3389/fcimb.2021.605825) and used for COG enrichment analysis.

Format

a vector with 134 COGs

Value

https://www.frontiersin.org/articles/10.3389/fcimb.2021.605825/full

Examples

data(Psoriasis_data)

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Example data: a vector of 91 KEGG Orthologies (KOs) showing significant associations with weaning weight

Description

This example data was reported on Fang S,et al.2019 (doi: 10.1111/1751-7915.13485) and used for KEGG enrichment analysis.

Format

a vector with 91 KEGG Orthologies (KOs)

References

https://sfamjournals.onlinelibrary.wiley.com/doi/10.1111/1751-7915.13485

Examples

data(Rat_data)

---

Run the Shiny Application

Description

Run the Shiny Application

Usage

run_MicrobiomeProfiler(
  onStart = NULL,
  options = list(),
  enableBookmarking = NULL,
  uiPattern = "/",
  ...
)

Arguments

onStart	A function that will be called before the app is actually run. This is only needed for shinyAppObj, since in the shinyAppDir case, a global.R file can be used for this purpose.
options	Named options that should be passed to the runApp call (these can be any of the following: "port", "launch.browser", "host", "quiet", "display.mode" and "test.mode"). You can also specify width and height parameters which provide a hint to the embedding environment about the ideal height/width for the app.
enableBookmarking	Can be one of "url", "server", or "disable". The default value, NULL, will respect the setting from any previous calls to enableBookmarking(). See enableBookmarking() for more information on bookmarking your app.
uiPattern	A regular expression that will be applied to each GET request to determine whether the ui should be used to handle the request. Note that the entire request path must match the regular expression in order for the match to be considered successful.
...	arguments to pass to golem_opts. See '?golem::get_golem_options' for more details.

Value

Shiny application object.

Examples

if (interactive()) {run_MicrobiomeProfiler()}

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