preparerewiring {TraRe} | R Documentation

## Prepare rewiring data for running the method.

### Description

Prepare neccessary files for running `runrewiring()`

### Usage

    preparerewiring(
      name = "defaultname",
      linker_output_p,
      lognorm_est_counts_p = NULL,
      SEObject_p = NULL,
      gene_info_p = NULL,
      phenotype_p = NULL,
      nassays = 1,
      final_signif_thresh = 0.001,
      regulator_info_col_name = "regulator",
      phenotype_col_name = "Class",
      phenotype_class_vals_string = "NR,R",
      phenotype_class_vals_string_label = "0,1",
      orig_test_perms = 100,
      retest_thresh = 0.08,
      retest_perms = 1000,
      outdir = tempdir(),
      nrcores = 3
    )

### Arguments

`name` | Desired name of the folder which is generated. The chosen threshold will be `paste()` to the folder's name.
`linker_output_p` | Output file from linker function path. RDS format is required.
`lognorm_est_counts_p` | Lognorm counts of the gene expression matrix path.
`SEObject_p` | SummarizedExperiment objects path.
`gene_info_p` | path of a two-column file containing genes and 'regulator' boolean variable.
`phenotype_p` | path of a two-column file containing used samples and Responder or No Responder 'Class' (NR,R).
`nassays` | name of assays in case SummarizedObject is provided.
`final_signif_thresh` | Significance threshold for the rewiring method. The lower the threshold, the restrictive the method.
`regulator_info_col_name` | Column name of the gene_info_p. By default, 'regulator'.
`phenotype_col_name` | Column name of the phenotype_p. By default, 'Class'.
`phenotype_class_vals_string` | Boolean terms of the phenotype_p at the 'Class' column. By default, (NR,R).
`phenotype_class_vals_string_label` | Boolean terms of the phenotype_p values at the 'Class' column. By default (0,1)
`orig_test_perms` | Initial permutations for first test (default: 100) .
`retest_thresh` | Threshold if a second test is performed (default: 0.08) .
`retest_perms` | Permutations if a second test is performed (default: 1000) .
`outdir` | Directory for the output folder to be located (default: tempdir())
`nrcores` | Number of cores to run the parallelization within the rewiring test (default: 3).

### Value

Return a list containing: LINKER's output, expression matrix, boolean array from phenotype file, array containing number of c(R,NR) samples, significance threshold and output directory.

### Examples

    ## We are going to prepare 4 files that we have in the example folder: the output from LINKER, the
    ## gene expression matrix, the phenotype file and the gene info file. Note that the LINKER
    ## output is generated from the gene expression matrix. Note: if rewiring across more than 1 dataset
    ## is desired, paths will be given as arrays. (i.e. linker_output <- c(path1,path2))

    linker_output_p <- paste0(system.file('extdata',package='TraRe'),'/linker_rewiring_example.rds')

    lognorm_est_counts_p <- paste0(system.file('extdata',package='TraRe'),
                            '/expression_rewiring_example.txt')

    gene_info_p <- paste0(system.file('extdata',package='TraRe'),'/geneinfo_rewiring_example.txt')

    phenotype_p <- paste0(system.file('extdata',package='TraRe'),'/phenotype_rewiring_example.txt')

    outdir <- system.file('extdata',package='TraRe')

    prepared <- preparerewiring(name='example',linker_output_p=linker_output_p,
                                lognorm_est_counts_p=lognorm_est_counts_p,gene_info_p=gene_info_p,
                                phenotype_p=phenotype_p,final_signif_thresh=0.05,
                                nrcores=1,outdir=outdir)

[Package TraRe version 1.2.0 Index]