Obtained the stacked-taxa table — getStackedTaxaMatrix • C3NA

Generate the stacked-taxa tabel for other correlation methods calculation outside C3NA.

getStackedTaxaMatrix(
  prevTrh = 0.1,
  phyloseqObj = phyloseqObj,
  nMinTotalCount = 1000,
  phenotype = NA
)

Arguments

prevTrh: (Required) Prevalence threshold of the samples, which is a number between 0 and 1. E.g., the default 0.1 represents 10% of the samples need to have given taxa.
phyloseqObj: (Required) Phyloseq phyloseq object. This should first undergo validatePhyloseq to ensure the diagnosis column are present.
nMinTotalCount: (Required) The Minimal number of reads per sample. Default: 1,000.
phenotype: (Required) The desired phenotype that present under the diagnosis column in the metadata from phyloseqObj

Value

countMatrix

Examples

data(CRC_Phyloseq)
curPhyloseq = validatePhloseq(phyloseqObj = CRC_Phyloseq)

# These steps are commented out due to time consuming step. The post sparcc correlation data will be 
# to avoid the step
# phyloseq_Cancer = phyloseq::subset_samples(physeq = CRC_Phyloseq, diagnosis == "Cancer")
# stackedTaxaMatrix = getStackedTaxaMatrix(phyloseqObj = phyloseq_Cancer, phenotype = "Cancer")

# Correlation method
# testCorMatrix = cor(t(stackedTaxaMatrix))