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 1.0.0 Index]