bamVarName: Get library variable names from ORFik 'experiment'

Description Usage Arguments Value See Also Examples

View source: R/experiment.R

Description

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

Usage

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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), don't include replicate in variable name.

skip.condition

a logical (FALSE), don't include condition in variable name.

skip.stage

a logical (FALSE), don't include stage in variable name.

skip.fraction

a logical (FALSE), don't include fraction

skip.experiment

a logical (FALSE), don't include experiment

skip.libtype

a logical (FALSE), don't include libtype

Value

variable names of libraries (character vector)

See Also

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

Examples

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

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

ORFik documentation built on March 27, 2021, 6 p.m.