degCorCov {DEGreport}R Documentation

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))

[Package DEGreport version 1.29.0 Index]