pairedCor: Correlate abundance of features between paired samples

In microresearcher/MicroVis: Microbiome Analysis and Visualization

Correlate abundance of features between paired samples

Description

Correlate abundance of features between paired samples

Usage

pairedCor(
  dataset = NULL,
  ids,
  compare,
  fts = NULL,
  rank = NULL,
  rthresh = 0.7,
  alpha = 0.05,
  padj = T,
  data.paired = NULL,
  groups = NULL
)

Arguments

dataset	MicroVis dataset. Defaults to the active dataset
ids	Column(s) that uniquely identify each pair of samples
compare	Column with the 2 groups to correlate between. Each pair of samples has a sample in each of the two groups in this column. If there are more than 2 groups in the column, user will be asked to select 2 to compare
fts	Vector of features to correlate between the two sets
rank	Taxonomic rank at which to perform the paired correlation. Defaults to the second highest rank in the dataset
rthresh	R value cutoff for coloring the figures of each figure. Defaults to 0.7
alpha	Significance threshold. Defaults to 0.05
padj	Adjust the p-values for multiple testing? Defaults to TRUE
data.paired	Provide a dataframe with data already paired according to "ids" and "compare"
groups	If providing a data.paired dataframe, must provide groups as well

Value

Scatter plot with trendline

microresearcher/MicroVis documentation built on Feb. 8, 2024, 10:59 a.m.