createDistMat: Create distance matrix of all vs all protein melting profiles

In nkurzaw/Rtpca: Thermal proximity co-aggregation with R

Create distance matrix of all vs all protein melting profiles

Description

Create distance matrix of all vs all protein melting profiles

Usage

createDistMat(
  objList,
  rownameCol = NULL,
  summaryMethodStr = "median",
  distMethodStr = "euclidean"
)

Arguments

objList	list of objects suitable for the analysis, currently allowed classes of objects are: matrices, data.frames, tibbles and ExpressionSets
rownameCol	in case the input objects are tibbles this parameter takes in the name (character) of the column specifying protein names or ids
summaryMethodStr	character string indicating a method to use to summarize measurements across replicates, default is "median", other options are c("mean", "rbind")
distMethodStr	method to use within dist function, default is 'euclidean'

Value

a distance matrix of all pairwise protein melting profiles

Examples

library(Biobase)

m1 <- matrix(1:12, ncol = 4)
m2 <- matrix(2:13, ncol = 4)
m3 <- matrix(c(2:10, 1:7), ncol = 4)

rownames(m1) <- 1:3
rownames(m2) <- 2:4
rownames(m3) <- 2:5

colnames(m1) <- paste0("X", 1:4)
colnames(m2) <- paste0("X", 1:4)
colnames(m3) <- paste0("X", 1:4)

mat_list <- list(
    m1, m2, m3
)

createDistMat(mat_list)

expr1 <- ExpressionSet(m1)
expr2 <- ExpressionSet(m2)
expr3 <- ExpressionSet(m3)

exprSet_list <- list(
    expr1, expr2, expr3
)

createDistMat(exprSet_list)

nkurzaw/Rtpca documentation built on May 12, 2023, 2:10 p.m.