compareFeatures: Compare features' abundance obtained by prediction and...

In MMINP: Microbe-Metabolite Interactions-Based Metabolic Profiles Predictor

Compare features' abundance obtained by prediction and measurement.

Description

Compare features' abundance obtained by prediction and measurement.

Usage

compareFeatures(
  predicted,
  measured,
  method = "spearman",
  adjmethod = "fdr",
  rsignif = 0.3,
  psignif = 0.05
)

Arguments

predicted	A matrix or data frame. The feature table obtained by prediction.
measured	A matrix or data frame. The feature table obtained by measurement. The abundances are expected to be normalized (i.e. proportion) or be preprocessed by MMINP.preprocess.
method	A character string indicating which correlation coefficient is to be used for the cor.test. One of "pearson", "kendall", or "spearman", can be abbreviated.
adjmethod	A character string indicating correction method (p.adjust). One of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none", can be abbreviated.
rsignif	A numeric ranging from 0 to 1, the minimum correlation coefficient of features which considered as well-predicted features.
psignif	A numeric ranging from 0 to 1, the maximum adjusted p value of features which considered as well-predicted features.

Value

A list containing a table of correlation results and a vector of well-predicted features.

MMINP documentation built on July 5, 2022, 1:08 a.m.