accessors: Set of methods to access or to set slots of a Experiment

In GiBacci/expR:

Set of methods to access or to set slots of a Experiment

Description

step returns/set the step of analysis from a Experiment object.

setStep sets the step of analysis of an Experiment object.

N returns the number of samples.

files and output return the input/output files from a Experiment object. If object is a SingleEndSamples it will return a vector of files otherwise it will return a data frame with forward and reverse files.

setOutput is used ot change tho output of a given experiment. The value parameter must be a character vector (for single end experiments) or a character matrix with two columns (for paired end samples). In alternative it can be a function that will be used for building output names.

samples returns the samples from a Experiment object.

run returns the samples from a Experiment object.

nrun returns the number of run from a Experiment object.

output.exists returns TRUE for each output file that is found on the hard drive. If the experiment is a paired-end experiment, the method will return TRUE only if both forward and reverse output files exist.

input.exists returns TRUE for each input file that is found on the hard drive. If the experiment is a paired-end experiment, the method will return TRUE only if both forward and reverse input files exist.

up2date returns TRUE for each input and output file up to date. Namely, the timestamp of each input file must be smaller than its output file.

Usage

step(obj)

step(obj) <- value

setStep(obj, value)

N(obj)

files(obj)

output(obj)

setOutput(obj, value)

samples(obj)

run(obj)

nrun(obj)

output.exists(obj)

input.exists(obj)

up2date(obj)

Arguments

obj	Experiment
value	the value to set. For the setOutput function, value must be a character vector (or a matrix for paired samples) or a function
obj	Experiment
obj	Experiment
obj	Experiment

GiBacci/expR documentation built on Oct. 15, 2022, 12:15 a.m.