checkTableConsistency {compcodeR} | R Documentation

## Check consistency of input table to `runComparison`

### 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

[Package compcodeR version 1.26.1 Index]