make_summary_table: Make summary table

In Hide-Fun/metabarcode: matabar; tools for metabarcoding

Description

This function make summary tabel.

Usage

make_summary_table(
  .id,
  .funguild,
  .seq,
  .sample_info,
  .tax_pat = "unite",
  .taxon,
  .remove = T
)

Arguments

.id	siz002
.funguild	funguild
.seq	clustered.fasta
.sample_info	sample information
.tax_pat	UNITE DB or overall_genus or another. If you specify "manual"
.taxon	manual
.remove	remove size.

Examples

identify_list <- data.frame(
otu = c("otu1", "otu2"),
phylum = c("p1", "p2"),
order = c("o1", "o2"),
family = c("f1", "f2"),
genus = c("g1", "g2")
)

otu_table <- data.frame(
  samplename = c("id_sample1", "id_sample2"),
  otu1 = c(1, 0),
  otu2 = c(0, 39)
)

seq <- data.frame(
  otu = c("otu1", "otu2"),
  seq = c("seq1", "seq2")
)

sample_info <- data.frame(
  samplename = c("id_sample1", "id_sample2"),
  sample_info = c("sample_info1", "sample_info2")
)


summary <- make_summary_table(
  .id = "id",
  .funguild = funguild_db(otu_table, identify_list, c("phylum", "order", "family", "genus")),
  .seq = seq,
  .tax_pat = "manual",
  .taxon = c("phylum", "order", "family", "genus"),
  .sample_info = sample_info,
  .remove = FALSE
)

summary[[1]]
summary[[2]]

Hide-Fun/metabarcode documentation built on March 10, 2021, 11:27 p.m.