degCorCov: Calculate the correlation relationshipt among all covariates...

In lpantano/DEGreport: Report of DEG analysis

Calculate the correlation relationshipt among all covariates in the metadata table

Description

This function will calculate the correlation among all columns in the metadata

Usage

degCorCov(metadata, fdr = 0.05, use_pval = FALSE, ...)

Arguments

metadata	data.frame with samples metadata.
fdr	numeric value to use as cutoff to determine the minimum fdr to consider significant correlations between pcs and covariates.
use_pval	boolean to indicate to use p-value instead of FDR to hide non-significant correlation.
...	Parameters to pass to ComplexHeatmap::Heatmap().

Value

: list: a) cor, data.frame with pair-wise correlations, pvalues, FDR b) corMat, data.frame with correlation matrix c) fdrMat, data.frame with FDR matrix b) plot, Heatmap plot of correlation matrix

Author(s)

: Lorena Pantano, Kenneth Daily and Thanneer Malai Perumal

Examples

data(humanGender)
library(DESeq2)
idx <- c(1:10, 75:85)
dse <- DESeqDataSetFromMatrix(assays(humanGender)[[1]][1:1000, idx],
  colData(humanGender)[idx,], design=~group)
cor <- degCorCov(colData(dse))

lpantano/DEGreport documentation built on Feb. 28, 2024, 12:01 a.m.