convertListTophyloCompData: Convert a list with data and results to a 'phyloCompData'...

In csoneson/compcodeR: RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods

Convert a list with data and results to a phyloCompData object

Description

Given a list with data and results (resulting e.g. from compcodeR version 0.1.0), convert it to a phyloCompData object.

Usage

convertListTophyloCompData(inp.list)

Arguments

inp.list

A list with data and results, e.g. generated by compcodeR version 0.1.0.

Author(s)

Charlotte Soneson, Paul Bastide

Examples

tree <- ape::read.tree(
  text = "(((A1:0,A2:0,A3:0):1,B1:1):1,((C1:0,C2:0):1.5,(D1:0,D2:0):1.5):0.5);"
  )
count.matrix <- round(matrix(1000*runif(8000), 1000))
sample.annotations <- data.frame(condition = c(1, 1, 1, 1, 2, 2, 2, 2),
                                 id.species = c("A", "A", "A", "B", "C", "C", "D", "D"))
info.parameters <- list(dataset = "mydata", uID = "123456")
length.matrix <- round(matrix(1000*runif(8000), 1000))
colnames(count.matrix) <- colnames(length.matrix) <- rownames(sample.annotations) <- tree$tip.label
convertListTophyloCompData(list(count.matrix = count.matrix,
                                sample.annotations = sample.annotations,
                                info.parameters = list(dataset = "mydata", 
                                                       uID = "123456"),
                                tree = tree,
                                length.matrix = length.matrix))
                                 

csoneson/compcodeR documentation built on Oct. 25, 2023, 1:28 a.m.