checkTableConsistency: Check consistency of input table to 'runComparison'

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

Description

Check that the dataset, nbr.samples, repl and de.methods columns of a data frame are consistent with the information provided in the input files (given in the input.files column of the data frame). If there are inconsistencies or missing information in any of the columns, replace the given information with the information in the input files.

Usage

checkTableConsistency(file.table)

Arguments

file.table

A data frame with columns named input.files and (optionally) datasets, nbr.samples, repl, de.methods.

Value

Returns a consistent file table defining the result files that will be used as the basis for a method comparison.

Author(s)

Charlotte Soneson

Examples

tmpdir <- normalizePath(tempdir(), winslash = "/")
mydata.obj <- generateSyntheticData(dataset = "mydata", n.vars = 1000, 
                                    samples.per.cond = 5, n.diffexp = 100, 
                                    output.file = file.path(tmpdir, "mydata.rds"))
runDiffExp(data.file = file.path(tmpdir, "mydata.rds"), result.extent = "voom.limma", 
           Rmdfunction = "voom.limma.createRmd", output.directory = tmpdir, 
           norm.method = "TMM")
runDiffExp(data.file = file.path(tmpdir, "mydata.rds"), result.extent = "edgeR.exact", 
           Rmdfunction = "edgeR.exact.createRmd", output.directory = tmpdir, 
           norm.method = "TMM",
           trend.method = "movingave", disp.type = "tagwise")

## A correct table
file.table <- data.frame(input.files = file.path(tmpdir, 
                         c("mydata_voom.limma.rds", "mydata_edgeR.exact.rds")), 
                         datasets = c("mydata", "mydata"),
                         nbr.samples = c(5, 5),
                         repl = c(1, 1),
                         stringsAsFactors = FALSE)
new.table <- checkTableConsistency(file.table)
new.table

## An incorrect table
file.table <- data.frame(input.files = file.path(tmpdir, 
                         c("mydata_voom.limma.rds", "mydata_edgeR.exact.rds")), 
                         datasets = c("mydata", "mydata"),
                         nbr.samples = c(5, 3),
                         repl = c(2, 1),
                         stringsAsFactors = FALSE)
new.table <- checkTableConsistency(file.table)
new.table

## A table with missing information
file.table <- data.frame(input.files = file.path(tmpdir, 
                         c("mydata_voom.limma.rds", "mydata_edgeR.exact.rds")),
                         stringsAsFactors = FALSE)
new.table <- checkTableConsistency(file.table)
new.table

compcodeR documentation built on Nov. 10, 2020, 2 a.m.