FeatureCorr: feature correlation

In zc1286/Wham: Workflow Hub for Automated Metagenomic Exploration (WHAM!)

Description

Visualization of Wham upstream analysis

Usage

FeatureCorr(
  object,
  feature,
  group,
  UseDE.result = F,
  p.cutoff = 0.05,
  effect.size.range = c(0, 0),
  method = c("pearson", "spearman", "kendall"),
  adjust = c("holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none"),
  count = c("rawCount", "WhamTransformation")
)

Arguments

object	required. The output of WhamBiobakery, WhamEBI or Wham16s
feature	default is NULL. if not provided and UseDE.result is FALSE, all features will be used.
group	default is NULL. if not provided and UseDE.result is FALSE, all samples will be used
UseDE.result	default value is FALSE. FALSE means using the argument feature and argument group. TRUE means using the features and samples from DE.result (after selection of parameters below).
p.cutoff	Keep genes whose we.eHB values are less than cutoff. The default value is 0.05. Use all gene from DE.result
effect.size.range	Keep genes whose effect size values are out of the range.The default value is c(0,0), Use all gene from DE.result. This only work when the aldex.module is set as t.test
method	the method of correlation. "spearman","pearson", and "kendall"
adjust	the method of multiple test correction. "holm","hochberg","hommel","bonferroni","BH","BY","fdr","none"
count	c("rawCount","WhamTransformation"). Default value is "rawCount". Setting as "rawCount" uses original count. Setting as WhamTransformation converts count to ratio(count divided by the total sum of each sample), and then times one million( x 1000,000)

Value

a correlation heatmap of gene family

Examples

# see the vignette for more details

zc1286/Wham documentation built on May 14, 2021, 8 p.m.