Match.Pattern: Match Patterns Function

In xia-lab/MicrobiomeAnalystR: MicrobiomeAnalystR - A comprehensive R package for statistical, visual, and functional analysis of the microbiome.

Match Patterns Function

Description

This functions matches patterns (when the defined pattern is set to a predefined profile or custom profile) in the Pattern Search analysis.

Usage

Match.Pattern(
  mbSetObj,
  dist.name = "pearson",
  pattern = NULL,
  taxrank,
  variable,
  appendname
)

Arguments

mbSetObj	Input the name of the mbSetObj.
dist.name	Input the distance measure. Input "pearson" for Pearson R, "spearman" for Spearman rank correlation, "kendall" for Kendall rank correlation and "sparcc" for SparCC.
pattern	Character, input the specified pattern.
taxrank	Character, input the taxonomic level to use.
variable	Input the name of the experimental factor.
taxa	If the pattern is defined by using a specific taxon, input the name of that taxa here.
datatype	If the data is marker gene, input "16S". If the data is metagenomic, use "metageno".
shotfeat	Only valid for SDP module, set to "null".
shotgunid	Only valid for SDP module, set to "NA".

Author(s)

Jeff Xia [e-mail] McGill University, Canada License: GNU GPL (>= 2)

xia-lab/MicrobiomeAnalystR documentation built on April 17, 2024, 7:45 p.m.