pre_tax_table: Complete a taxonomy table
In pctax: Professional Comprehensive Omics Data Analysis

pre_tax_table

R Documentation

Complete a taxonomy table

Description

Complete a taxonomy table

Usage

pre_tax_table(
  tax_table,
  tax_levels = c("k", "p", "c", "o", "f", "g", "s", "st"),
  na_tax = "Unclassified|uncultured|Ambiguous|Unknown|unknown|metagenome|Unassig",
  ignore.case = TRUE,
  na_repalce = "Unknown"
)

Arguments

`tax_table`	taxonomy table
`tax_levels`	a vector whose length longer than `ncol(taxdf)`, use to be prefix. Default: c("k", "p", "c", "o", "f", "g","s", "st")
`na_tax`	grepl some words and turn to `na_repalce`, default: "Unclassified\|uncultured\|Ambiguous\|Unknown\|unknown\|metagenome\|Unassig"
`ignore.case`	ignore.case for `na_tax`
`na_repalce`	defalut: Unknown

Value

a good taxonomy table

References

MicrobiotaProcess

Examples

taxmat <- matrix(sample("onelevel", 7 * 2, replace = TRUE), nrow = 2, ncol = 7) %>% as.data.frame()
colnames(taxmat) <- c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species")
pre_tax_table(taxmat)

pctax documentation built on May 29, 2024, 10:03 a.m.