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Function browseGenome [rtracklayer v1.32.1]
keywords
interface
title
Browse a genome
description
A generic function for launching a genome browser.
Function genomeBrowsers [rtracklayer v1.32.1]
keywords
interface
title
Get available genome browsers
description
Gets the identifiers of the loaded genome browser drivers.
Function ucscGenomes [rtracklayer v1.32.1]
keywords
interface
title
Get available genomes on UCSC
description
Get a data.frame describing the available UCSC genomes.
Function msplit [batch v1.1-5]
keywords
interface
title
Split Vectors for Parallelization
description
Aids in splitting of a vector for parallelization, e.g. splitting up a group of SNPs into subgroups, so each one can analyzed in a parallel process. Other uses might be to choose splitting points for k-fold cross validation.
Function parseCommandArgs [batch v1.1-5]
keywords
interface
title
Parse Command-Line Arguments
description
parseCommandArgs allows for command line arguments to be passed into R. Arguments may be of the form of simple R objects. This makes running the same R code on multiple different options easy, and possible to run in parallel on a single machine or on a cluster. parseCommandArgsDF returns a dataframe with all of the values that were set when the code was executed.
Function rbatch [batch v1.1-5]
keywords
interface
title
R Batch Submission
description
Aids in the submission of multiple jobs to a cluster. Also can be used locally on a linux machine to utilize all cores (or processors), if the cluster is busy.
Function mergeCsv [batch v1.1-5]
keywords
interface
title
Merge CSV Files
description
Merges multiple csv's in the current directory together, with the option of averaging over several. For instance, if you have broken a set of simulations each into five jobs, this will merge all groups of five simulations together.
Function phe [pbatR v2.2-13]
keywords
interface
title
Phenotype Object
description
Creates, tests, reads, or writes an object of class phe.
Function clean [pbatR v2.2-13]
keywords
interface
title
Cleaning pbat(), pbat.last(), pbat.m() output.
description
Removes many of the temporary output files from communicating with PBAT. Make sure you save how PBAT was run for future reference. Most useful for simulations.
Function cluster [pbatR v2.2-13]
keywords
interface
title
Cluster result functions
description
Options when 'clusterRefresh' has been set to 0 (so that the current process is batched). See pbat.set for details. is.finished() returns if PBAT execution has terminated. pbat.load() loads in PBAT output. pbat.concatenate() concatenates output files (without reading them into an R object).