bamVarName {ORFik}

R Documentation

Get library variable names from ORFik experiment

Description

What will each sample be called given the columns of the experiment?

Usage

bamVarName(
  df,
  skip.replicate = length(unique(df$rep)) == 1,
  skip.condition = length(unique(df$condition)) == 1,
  skip.stage = length(unique(df$stage)) == 1,
  skip.fraction = length(unique(df$fraction)) == 1,
  skip.experiment = !df@expInVarName,
  skip.libtype = FALSE
)

Arguments

df	an ORFik experiment
skip.replicate	a logical (FALSE), if TRUE don't include replicate in variable name.
skip.condition	a logical (FALSE), if TRUE don't include condition in variable name.
skip.stage	a logical (FALSE), if TRUE don't include stage in variable name.
skip.fraction	a logical (FALSE), if TRUE don't include fraction
skip.experiment	a logical (!df@expInVarName), if TRUE don't include experiment
skip.libtype	a logical (FALSE), if TRUE don't include libtype

Value

variable names of libraries (character vector)

See Also

Other ORFik_experiment: ORFik.template.experiment.zf(), ORFik.template.experiment(), create.experiment(), experiment-class, filepath(), libraryTypes(), organism,experiment-method, outputLibs(), read.experiment(), save.experiment(), validateExperiments()

Examples

df <- ORFik.template.experiment()
bamVarName(df)

## without libtype
bamVarName(df, skip.libtype = TRUE)
## Without experiment name
bamVarName(df, skip.experiment = TRUE)

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