format_hits: Format differential test results to be presentable

In TBrach/MicrobiomeX: eXtended Functions for Microbiome Analysis and Visualization

Description

Format differential abundance/prevalence results for elegant presentation, selecting only the significant hits.

Usage

format_hits(results, p.adjust.threshold = 0.1, p.adjust.method = NULL)

Arguments

results	Results from test_differential_abundance_DESeq2(), or test_differential_abundance_Wilcoxon() or test_differential_prevalence().
p.adjust.threshold	Adjusted P-value threshold to use when returning the significant hits.
p.adjust.method	P-value adjustment method, in case you want it to be re-estimated. Use this only if you know what you are doing!!

Value

Returns a list containing all the entities in the input results variable, with the following changes:

• table: Data frame consisting of taxa that pass given FDR threshold, with names formatted for elegant presentation. All hits up to and including the P-value threshold will be returned. Columns depend on the type of results.
  Common columns are: Taxon, Annotation, padj, Significance, Direction.
  Depending on the result type, the following extra columns will be present:

  • Prevalence test: OR, OR_CE

  • DESeq2: log2FC

  • Wilcoxon: Med_1, Med_2

• nhits: Number of significant hits that pass the threshold for adjusted P-value.

Examples

## Not run: 

# Run DESeq2

x <- test_differential_abundance_DESeq2(physeq, group = "Health_status", compare = c("T2D", "Healthy"))
y <- format_hits(x, p.adjust.method= "bonferroni") # Overwrite DESeq's FDR padj with Bonferroni padj
z <- format_hits_for_heatmap(y)
draw_taxa_heatmap(physeq, taxa_data = z, group = "Health_status", compare = c("T2D", "Healthy"))

# Run Wilcoxon rank sum test

x <- test_differential_abundance_Wilcoxon(physeq, group = "Health_status")
y <- format_hits(x)
z <- format_hits_for_heatmap(y)
draw_taxa_heatmap(physeq, taxa_data = z, group = "Health_status", block = "Enterotype")

# Set up custom palette
pal = list(Health_status = "Set2", Enterotype = "Pastel1", Significance = "PuRd")

# Run differential prevalence test

x <- test_differential_prevalence(physeq, group = "Health_status")
y <- format_hits(x)
z <- format_hits_for_heatmap(y, p.adjust.threshold = 0.01)
draw_taxa_heatmap(physeq, taxa_data = z, group = "Health_status", custom_palette = pal)

## End(Not run)

TBrach/MicrobiomeX documentation built on May 14, 2019, 2:28 p.m.