pcor_dat: Partial correlation analysis

In wanchanglin/mtExtra: More functions for metabolomics data analysis

Partial correlation analysis

Description

Perform partial correlation analysis of two data matrix

Usage

pcor_dat(x, y, method = c("pearson", "kendall", "spearman"))

Arguments

x, y	two data matrix for correlation analyses.
method	correlation method.

Value

a correlation matrix.

See Also

ppcor::pcor()

Examples

library(dplyr)
library(tidyr)
library(purrr)

## 'data' has been processed.
data <- mtExtra:::data
meta <- mtExtra:::meta

## filtering
meta <- mv_filter(meta, thres = 0.3)$dat

## missing value filling
meta <- meta %>%
  mutate(across(where(is.numeric), function(x) {
    m <- mean(x, na.rm = TRUE)
    x[is.na(x)] <- m
    x
  }))

## normalisation
meta <- meta %>% 
  mutate(across(where(is.numeric), ~ {
    .x <- (.x - mean(.x, na.rm = TRUE)) / sd(.x, na.rm = TRUE)
  }))

co <- pcor_dat(meta, data) 
heat_dend(co)

wanchanglin/mtExtra documentation built on Aug. 2, 2024, 5:47 p.m.